Contacts of the helix formed by residues 289 - 310 (chain A) in PDB entry 3U8Z
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 289 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASP* 5.4 10.3 + - - +
71A THR* 4.8 4.8 + - - +
287A SER* 3.5 2.0 + - - -
288A SER* 1.4 85.9 + - - +
290A LEU* 1.3 59.8 + - - +
291A ARG* 3.6 38.8 - - - +
292A VAL* 3.4 31.0 + - + +
293A ASN* 3.1 31.9 + - - +
124B LYS* 5.1 8.4 - - - +
128B ASP* 3.3 36.8 + - - +
130B LYS* 4.8 7.9 - - - +
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A TYR* 3.5 29.8 - - + +
269A LYS* 5.2 10.4 - - + +
288A SER 3.9 3.0 + - - -
289A LYS* 1.3 68.6 - - - +
291A ARG* 1.4 68.1 + - - +
293A ASN* 3.1 7.9 + - + +
294A LYS* 3.1 51.4 + - + +
178C GLN 6.2 1.1 - - - +
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 4.6 22.1 + - + -
69A LYS* 4.6 24.3 - - - +
70A ASP* 5.8 2.0 - - - +
71A THR* 3.2 36.7 + - + +
72A VAL 5.0 1.9 - - - +
289A LYS* 3.6 46.2 - - + +
290A LEU* 1.4 81.5 - - - +
292A VAL* 1.4 63.1 + - + +
294A LYS* 3.8 13.9 + - - +
295A LEU* 3.5 17.8 + - - +
124B LYS* 5.7 4.9 - - - +
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Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A THR* 3.7 23.6 - - + +
222A PHE* 3.5 33.0 - - + -
287A SER* 4.4 7.4 - - - +
289A LYS* 3.4 39.2 + - + +
290A LEU 3.3 0.6 - - - -
291A ARG* 1.4 75.7 - - - +
293A ASN* 1.3 56.6 + - - +
295A LEU* 3.1 8.0 + - + +
296A ILE* 2.9 33.5 + - + +
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Residues in contact with ASN 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A TYR* 2.7 37.8 + - + +
269A LYS* 4.0 3.4 - - - +
271A PHE* 3.6 21.9 - - + -
287A SER* 2.8 50.3 + - - -
289A LYS 3.1 15.0 + - - +
290A LEU* 3.1 10.2 + - + +
292A VAL* 1.3 76.4 - - - +
294A LYS* 1.4 59.2 + - + +
296A ILE* 3.5 5.1 + - - +
297A LEU* 3.2 30.1 + - - +
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Residues in contact with LYS 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LEU* 3.1 43.2 + - + +
291A ARG* 3.8 15.3 - - - +
292A VAL 3.3 0.2 - - - -
293A ASN* 1.4 74.1 - - + +
295A LEU* 1.3 62.3 + - - +
297A LEU* 3.5 9.3 + - + +
298A GLN* 3.1 36.4 + - - +
187C ARG* 5.1 1.3 + - - +
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A THR* 5.0 5.4 - - + -
72A VAL* 3.8 38.1 - - + +
74A TRP* 3.6 34.3 - - + +
99A LYS* 4.7 0.2 - - - -
222A PHE* 4.3 16.6 - - + -
291A ARG 3.5 10.1 + - - +
292A VAL* 3.1 11.1 + - + +
294A LYS* 1.3 76.5 - - - +
296A ILE* 1.4 64.2 + - - +
298A GLN* 3.2 14.5 + - - +
299A LEU* 3.0 48.8 + - + +
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Residues in contact with ILE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A PHE* 3.6 50.0 - - + -
224A ILE* 5.4 0.4 - - + -
234A LEU* 3.8 24.5 - - + -
236A VAL* 4.4 2.8 - - + +
271A PHE* 3.6 34.5 - - + -
285A PHE* 5.3 1.6 - - + -
287A SER* 4.2 7.6 - - - +
292A VAL* 2.9 25.4 + - + +
293A ASN* 3.7 12.8 - - - +
294A LYS 3.5 0.2 - - - -
295A LEU* 1.4 73.3 - - - +
297A LEU* 1.3 57.6 + - - +
299A LEU* 3.2 5.8 + - - +
300A CYS* 2.9 42.3 + - - -
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ILE* 4.3 7.4 - - + -
266A TYR* 3.9 28.9 - - + -
271A PHE* 3.7 24.0 - - + -
293A ASN 3.2 19.3 + - - +
294A LYS* 3.9 8.1 - - + +
295A LEU 3.3 0.4 - - - -
296A ILE* 1.3 73.1 - - - +
298A GLN* 1.4 64.6 + - - +
300A CYS* 3.2 10.0 + - + +
301A ILE* 3.0 33.8 + - + +
178C GLN 5.4 1.6 - - - +
179C MET* 3.6 40.2 - - + -
184C TRP* 5.6 0.2 - - + -
187C ARG* 4.1 15.3 - - - +
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Residues in contact with GLN 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 4.0 16.0 + - - +
76A LYS* 4.4 23.6 - - - +
99A LYS* 3.1 31.8 + - - +
100A PHE* 4.0 9.0 - - - -
294A LYS* 3.1 25.2 + - - +
295A LEU* 3.4 22.0 - - - +
297A LEU* 1.4 76.0 - - - +
299A LEU* 1.3 59.9 + - - +
301A ILE* 3.5 7.9 + - - +
302A GLY 3.2 18.5 + - - -
187C ARG* 4.5 9.8 - - - +
191C TRP* 5.2 2.1 + - - -
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 5.3 0.7 - - - +
99A LYS* 3.8 44.4 - - + +
100A PHE* 4.0 8.1 - - + -
220A ASN* 3.7 27.4 - - + +
222A PHE* 3.6 32.3 - - + -
236A VAL* 3.9 12.8 - - + -
295A LEU* 3.0 31.2 + - + +
296A ILE 3.6 5.8 - - - +
298A GLN* 1.3 72.4 - - - +
300A CYS* 1.3 65.2 + - - +
303A ASN* 2.7 33.8 + - - +
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Residues in contact with CYS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A VAL* 4.2 3.6 - - - -
241A LEU* 3.8 33.0 - - - -
258A TRP* 3.4 16.7 - - + -
264A ILE* 4.6 6.7 - - + -
271A PHE* 5.9 0.9 - - - -
296A ILE* 2.9 37.8 + - - -
297A LEU* 3.2 16.1 + - + +
299A LEU* 1.3 76.3 - - - +
301A ILE* 1.4 56.6 + - - +
304A HIS* 3.0 32.2 + - - +
184C TRP* 3.9 17.9 - - + -
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Residues in contact with ILE 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU 3.0 23.3 + - - +
298A GLN* 3.9 5.6 - - - +
299A LEU 3.4 0.2 - - - -
300A CYS* 1.4 74.5 - - - +
302A GLY* 1.3 63.2 + - - +
304A HIS* 3.4 1.0 + - - +
305A ASP* 3.1 25.5 + - - +
179C MET* 4.8 3.1 - - - -
184C TRP* 3.8 20.9 - - + -
187C ARG* 3.1 72.5 - - + +
188C ILE* 3.9 15.3 - - + -
191C TRP* 3.6 23.8 - - + -
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Residues in contact with GLY 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A PHE* 3.6 21.8 - - - -
298A GLN 3.2 7.9 + - - -
301A ILE* 1.3 78.9 - - - +
303A ASN* 1.3 57.9 + - - +
305A ASP* 3.3 2.6 + - - +
306A LEU* 3.0 34.2 + - - +
191C TRP* 3.6 25.8 - - - +
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Residues in contact with ASN 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE* 3.7 27.5 - - - +
101A TYR 4.9 4.5 + - - +
220A ASN* 4.6 7.1 - - - +
236A VAL* 3.9 11.5 - - - +
237A ASP* 3.5 34.4 + - - +
238A ALA* 3.7 11.1 + - - +
258A TRP* 3.6 10.8 + - + +
299A LEU* 2.7 35.0 + - - +
302A GLY* 1.3 71.0 - - - +
304A HIS* 1.3 60.5 + - - +
306A LEU* 4.0 5.5 - - - +
307A PHE* 3.0 30.7 + - - +
310A ARG* 4.9 1.4 + - - +
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Residues in contact with HIS 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A TRP* 3.7 50.7 + + + -
261A ILE* 5.5 4.0 + - + -
300A CYS 3.0 21.5 + - - +
301A ILE 3.5 4.7 - - - +
303A ASN* 1.3 76.1 - - - +
305A ASP* 1.3 75.6 + - - +
307A PHE* 3.3 4.5 - - - +
308A MET* 3.1 51.8 + - + +
184C TRP* 4.1 16.5 + + + -
185C GLU* 5.9 1.1 - - - -
188C ILE* 3.7 28.2 - - + +
192C TYR* 4.3 0.9 - - - -
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Residues in contact with ASP 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A ILE 3.1 15.6 + - - +
302A GLY 3.3 0.6 + - - +
304A HIS* 1.3 94.2 + - - +
306A LEU* 1.3 65.4 + - - +
308A MET 3.4 1.0 + - - -
309A ARG* 3.1 21.5 + - - +
188C ILE* 2.6 37.2 - - - +
191C TRP* 3.2 37.4 - - + +
192C TYR* 3.5 34.3 + - + -
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TRP* 3.7 32.1 - - + +
61A PHE* 4.9 1.1 - - + -
100A PHE* 3.7 34.8 - - + -
101A TYR 5.3 0.2 - - - +
302A GLY 3.0 21.2 + - - +
303A ASN* 4.2 5.4 - - - +
305A ASP* 1.3 73.0 - - - +
307A PHE* 1.3 64.7 + - - +
309A ARG* 3.5 20.3 + - + +
310A ARG* 3.2 56.2 + - - +
191C TRP* 3.7 24.0 - - + -
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Residues in contact with PHE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLU* 4.0 2.0 - - - -
238A ALA 3.3 18.8 - - - +
239A LEU* 3.8 20.0 - - + -
257A PRO* 5.3 0.9 - - + -
258A TRP* 3.6 22.2 - + + -
259A ASN* 3.3 46.2 - - + -
303A ASN 3.0 19.9 + - - +
304A HIS 3.3 4.9 - - - +
306A LEU* 1.3 75.6 - - - +
308A MET* 1.3 73.2 + - - +
310A ARG* 3.4 14.0 + - - +
311A ARG* 2.9 73.7 + - - +
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Residues in contact with MET 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A TRP 5.3 0.2 - - - +
259A ASN* 4.9 11.4 - - + -
304A HIS* 3.1 35.6 + - + +
305A ASP 3.7 1.3 - - - +
306A LEU 3.3 0.4 - - - -
307A PHE* 1.3 96.5 - - - +
309A ARG* 1.4 63.6 + - - +
311A ARG* 3.1 21.9 + - + +
312A LYS 3.4 14.2 + - - +
192C TYR* 3.3 26.2 - - + +
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Residues in contact with ARG 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TRP* 4.8 11.5 - - - -
305A ASP 3.1 19.1 + - - +
306A LEU* 3.8 22.0 - - + +
307A PHE 3.4 0.2 - - - -
308A MET* 1.4 76.0 - - - +
310A ARG* 1.3 58.3 + - + +
312A LYS* 3.2 26.2 + - - +
191C TRP* 4.1 16.2 - - - -
192C TYR* 3.0 45.5 + - + +
195C HIS 2.7 30.9 + - - -
196C ARG* 4.4 7.7 - - - +
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Residues in contact with ARG 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 4.1 8.5 - - - -
101A TYR 3.2 21.6 + - - -
102A PRO* 3.7 0.8 - - - +
103A GLU* 3.0 38.5 + - - -
108A GLU* 3.0 41.3 + - + +
238A ALA* 3.9 15.2 + - - +
303A ASN* 4.9 1.8 + - - +
306A LEU* 3.2 42.7 + - - +
307A PHE* 3.6 11.3 - - - +
308A MET 3.3 0.2 - - - -
309A ARG* 1.3 76.1 - - + +
311A ARG* 1.3 68.2 + - - +
312A LYS* 3.3 8.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il