Contacts of the helix formed by residues 289 - 310 (chain A) in PDB entry 2CXQ
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 GLY 289 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ARG* 3.3 25.8 - - - +
285A ALA 2.8 18.4 + - - +
288A VAL* 1.3 82.2 - - - +
290A PHE* 1.3 65.3 + - - -
291A ASP* 3.3 3.6 - - - -
292A HIS* 3.3 3.7 + - - +
293A PHE* 3.1 18.9 + - - +
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Residues in contact with PHE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 3.3 45.8 - - + -
127A ASP* 6.0 0.4 - - - -
129A MET* 3.9 10.1 - - + -
130A LYS* 3.6 50.5 - - + +
133A CYS* 4.5 11.8 - - + +
137A ARG* 5.0 0.4 - - - +
285A ALA* 3.5 20.1 + - + -
289A GLY* 1.3 69.6 - - - -
291A ASP* 1.3 63.7 + - - +
293A PHE* 3.1 19.7 + + - +
294A GLU* 2.8 63.9 + - + +
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Residues in contact with ASP 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LYS* 5.2 8.1 + - - -
289A GLY* 3.3 1.3 - - - -
290A PHE* 1.3 81.2 - - - +
292A HIS* 1.3 59.7 + - + +
294A GLU* 3.3 19.8 + - - +
295A GLN* 3.0 40.2 + - - +
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Residues in contact with HIS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 5.3 0.6 - - - +
174A TYR* 3.6 36.6 - + + +
288A VAL* 2.8 39.6 + - + +
289A GLY* 3.3 3.5 + - - +
290A PHE 3.3 0.4 - - - -
291A ASP* 1.3 76.4 - - + +
293A PHE* 1.3 60.2 + - - +
295A GLN* 3.2 29.6 + - - -
296A LEU* 3.0 24.6 + - - +
484A PRO* 3.4 28.1 - - + +
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Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 3.9 17.9 - - + -
129A MET* 3.7 18.4 - - + -
276A LEU 3.5 26.7 - - - -
277A TRP 3.8 13.5 - - - -
278A SER 3.8 8.1 - - - -
281A GLY* 3.9 10.8 - - - -
284A ILE* 3.9 25.8 - - + -
285A ALA* 3.8 17.3 - - + +
288A VAL* 4.6 0.6 - - - +
289A GLY 3.1 11.9 + - - +
290A PHE* 3.1 27.7 + + - +
292A HIS* 1.3 76.7 - - - +
294A GLU* 1.3 57.8 + - - +
296A LEU* 3.2 23.1 + - + +
297A LEU* 3.0 40.1 + - + +
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Residues in contact with GLU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ARG* 3.1 33.7 + - - +
130A LYS* 5.1 7.8 + - - -
290A PHE* 2.8 44.8 + - + +
291A ASP* 3.3 24.4 + - - +
293A PHE* 1.3 76.4 - - - +
295A GLN* 1.3 55.7 + - + +
297A LEU* 3.4 12.4 + - + +
298A SER* 2.9 33.3 + - - +
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Residues in contact with GLN 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ASP* 3.0 29.3 + - - +
292A HIS* 3.2 34.7 + - - +
294A GLU* 1.3 73.0 - - + +
296A LEU* 1.3 60.9 + - - +
298A SER* 3.2 8.4 + - - -
299A GLY 2.9 24.8 + - - -
484A PRO* 3.9 15.9 - - + +
485A PHE* 3.3 21.8 + - + +
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A VAL* 4.2 17.3 - - + -
171A LEU* 4.5 3.6 - - + -
276A LEU* 3.9 24.7 - - + -
277A TRP* 3.7 13.0 - - + -
284A ILE* 4.5 2.5 - - + -
292A HIS 3.0 12.5 + - - +
293A PHE* 3.3 31.4 - - + +
295A GLN* 1.3 75.8 - - - +
297A LEU* 1.3 61.1 + - - +
299A GLY 3.3 1.6 + - - -
300A ALA 3.2 17.0 + - - -
484A PRO* 3.4 25.0 + - + +
487A LEU* 4.1 21.5 - - + -
488A GLY* 3.4 27.2 - - - +
491A ILE* 4.6 4.5 - - + -
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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
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103A LEU 4.2 9.6 - - - +
104A ARG* 3.4 24.4 - - + +
106A ARG* 3.9 25.6 - - - +
126A LEU* 3.8 28.5 - - + -
277A TRP* 3.5 49.6 - - + +
293A PHE* 3.0 31.3 + - + +
294A GLU* 3.6 10.8 - - + +
296A LEU* 1.3 75.0 - - + +
298A SER* 1.3 57.8 + - - +
300A ALA 3.3 1.7 + - - -
301A HIS* 2.9 25.3 + - - +
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Residues in contact with SER 298 (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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106A ARG* 3.7 29.1 + - - +
294A GLU* 2.9 23.7 + - - +
295A GLN* 3.2 8.7 + - - -
297A LEU* 1.3 75.4 - - - +
299A GLY* 1.3 57.1 + - - +
301A HIS* 3.3 3.1 + - - +
302A TRP* 2.9 24.8 + - - +
485A PHE* 3.6 19.9 - - - -
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Residues in contact with GLY 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLN 2.9 11.1 + - - -
296A LEU 3.3 1.3 + - - -
298A SER* 1.3 73.5 - - - +
300A ALA* 1.3 63.9 + - - +
302A TRP* 3.2 2.9 + - - +
303A MET 3.1 17.0 + - - -
485A PHE* 3.2 40.7 - - - -
489A ALA* 3.4 18.4 - - - +
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Residues in contact with ALA 300 (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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104A ARG* 3.7 18.8 - - - +
277A TRP* 3.5 33.9 - - + -
296A LEU 3.2 5.7 + - - -
297A LEU 3.5 6.7 - - - +
299A GLY* 1.3 74.2 - - - +
301A HIS* 1.3 57.9 + - - +
303A MET* 3.1 4.0 + - - +
304A ASP* 2.8 33.9 + - - +
488A GLY 3.4 15.2 - - - +
492A ALA* 3.8 7.4 - - + +
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Residues in contact with HIS 301 (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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101A VAL 5.3 0.4 + - - -
104A ARG* 3.1 26.8 + - - +
105A ASN* 3.5 26.1 - - - -
106A ARG* 3.7 21.7 + - + -
107A SER* 3.8 18.8 + - - -
297A LEU 2.9 9.7 + - - +
298A SER* 3.5 9.0 - - - +
300A ALA* 1.3 77.0 - - - +
302A TRP* 1.3 63.1 + - - +
304A ASP* 3.2 14.4 + - + +
305A GLN* 3.0 55.6 + - + +
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Residues in contact with TRP 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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44A LEU* 3.9 27.1 - - + -
45A ASN 3.5 19.6 + - - -
46A THR* 3.5 44.0 + - + +
47A ASN* 4.9 4.8 - - - +
51A ILE* 5.4 0.2 - - + -
298A SER 2.9 14.1 + - - +
299A GLY 3.5 8.5 - - - +
301A HIS* 1.3 76.6 - - - +
303A MET* 1.3 82.9 + - + +
305A GLN* 3.2 9.1 + - + +
306A HIS* 2.9 51.8 + - + -
485A PHE* 3.8 16.2 - + + -
489A ALA* 5.0 2.5 - - + -
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Residues in contact with MET 303 (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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44A LEU* 4.3 10.3 - - + -
51A ILE* 4.4 7.0 - - + -
299A GLY 3.1 6.7 + - - +
300A ALA 3.1 8.5 + - - +
302A TRP* 1.3 98.0 - - + +
304A ASP* 1.3 60.3 + - - +
306A HIS* 3.4 22.8 - - - +
307A PHE* 2.9 28.8 + - - +
317A PRO* 4.3 5.2 - - + -
489A ALA* 3.4 36.3 - - + +
492A ALA* 3.8 7.6 - - + +
493A MET* 3.5 45.1 - - + +
496A HIS* 4.7 3.1 - - + -
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Residues in contact with ASP 304 (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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85A PHE* 3.6 18.8 - - + -
101A VAL* 3.7 15.3 - - + +
104A ARG* 2.7 46.4 + - - +
300A ALA 2.8 18.3 + - - +
301A HIS* 3.2 15.1 + - - +
303A MET* 1.3 72.2 - - - +
305A GLN* 1.3 59.5 + - + +
307A PHE* 3.3 3.8 + - - +
308A LEU* 2.9 29.5 + - - +
492A ALA* 4.1 0.7 - - - +
496A HIS* 2.7 33.5 + - - -
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Residues in contact with GLN 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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85A PHE* 5.0 5.1 - - - -
107A SER* 5.7 1.2 + - - -
301A HIS* 3.0 45.2 + - + +
302A TRP* 3.6 10.3 - - + +
304A ASP* 1.3 76.2 - - - +
306A HIS* 1.3 64.2 + - - +
308A LEU* 3.9 19.4 - - - +
309A LYS* 3.0 53.4 + - + +
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Residues in contact with HIS 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 3.5 30.2 - - + +
302A TRP* 2.9 37.1 + + + +
303A MET* 3.4 17.3 - - - +
305A GLN* 1.3 77.1 - - - +
307A PHE* 1.3 63.5 + - - +
310A THR* 2.7 52.3 + - + -
314A LYS 3.7 13.0 - - - -
315A ASN* 3.7 3.2 - - - -
316A ALA* 3.0 33.5 + - + +
317A PRO* 3.8 14.4 - - + -
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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
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77A VAL* 5.1 3.4 - - + -
81A ARG* 2.9 45.4 + - + -
84A MET* 4.3 1.1 - - + -
85A PHE* 3.9 13.9 - + - -
303A MET 2.9 17.0 + - - +
304A ASP 3.5 3.6 - - - +
306A HIS* 1.3 78.4 - - - +
308A LEU* 1.3 57.2 + - - +
315A ASN* 2.9 36.5 + - - +
317A PRO* 3.7 11.4 - - + -
318A VAL* 3.8 10.5 - - + -
496A HIS* 3.3 47.1 - + + -
499A PHE* 3.7 27.4 - + - -
500A VAL* 3.7 23.3 - - + -
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Residues in contact with LEU 308 (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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81A ARG* 3.2 32.6 + - - +
82A ASP* 3.7 23.6 - - - +
85A PHE* 3.8 38.4 - - + -
304A ASP 2.9 16.3 + - - +
305A GLN* 3.8 22.4 - - - +
306A HIS 3.3 0.2 - - - -
307A PHE* 1.3 78.5 - - - +
309A LYS* 1.3 87.6 + - + +
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Residues in contact with LYS 309 (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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305A GLN* 3.0 40.3 + - + +
308A LEU* 1.3 102.2 - - + +
310A THR* 1.3 63.2 + - - +
311A PRO* 3.8 6.4 - - - +
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Residues in contact with THR 310 (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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81A ARG* 4.5 5.5 + - - -
306A HIS* 2.7 42.9 + - + -
307A PHE 4.4 0.5 - - - +
309A LYS* 1.3 78.8 - - - +
311A PRO* 1.3 82.4 - - + +
312A LEU* 3.4 2.1 + - - +
314A LYS* 3.3 33.9 - - + +
315A ASN* 2.9 22.0 + - - +
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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
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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) + - + + + + + -
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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