Contacts of the helix formed by residues 293 - 307 (chain A) in PDB entry 4K2S
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 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A TRP* 2.9 28.2 + - - -
85A MET* 3.7 32.7 + - - +
88A ILE* 4.7 0.7 - - - -
89A ALA* 3.7 7.9 - - - -
92A ASP* 4.0 2.8 - - - +
268A ASN 4.3 1.0 + - - -
289A LEU 3.7 0.8 + - - -
291A HIS 3.4 5.5 + - - -
292A GLY* 1.3 76.4 - - - +
294A GLY* 1.3 62.7 + - - +
297A ALA* 3.7 9.2 + - - +
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Residues in contact with GLY 294 (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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89A ALA* 3.3 16.1 - - - +
92A ASP* 3.8 4.9 - - - -
93A MET* 4.8 3.6 - - - -
289A LEU* 2.9 30.7 + - - -
292A GLY 3.4 0.2 - - - -
293A GLY* 1.3 78.1 - - - +
295A ILE* 1.3 59.2 + - - -
296A THR 3.3 0.2 - - - -
298A MET* 3.0 32.7 + - - +
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Residues in contact with ILE 295 (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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92A ASP* 2.9 4.0 + - - +
93A MET* 4.7 12.0 - - + +
96A TRP* 3.5 37.2 - - + +
107A LEU* 4.1 23.3 - - + -
111A LEU* 3.8 27.4 - - + -
289A LEU* 3.6 34.5 - - + +
294A GLY* 1.3 68.7 - - - -
296A THR* 1.3 67.6 + - - +
299A ARG* 3.0 29.5 + - + +
327A ALA* 4.4 3.8 - - + +
331A PHE* 4.0 17.8 - - + -
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Residues in contact with THR 296 (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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65A ILE* 3.6 7.3 - - - +
66A GLU* 3.9 16.5 + - - +
69A TRP* 3.8 22.2 - - + -
92A ASP* 2.6 32.9 + - - -
96A TRP* 3.0 18.6 + - - +
295A ILE* 1.3 79.6 - - - +
297A ALA* 1.3 61.3 + - - +
299A ARG* 3.9 6.2 - - - +
300A ARG* 3.3 44.1 + - - +
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TRP* 3.7 23.8 - - + -
85A MET* 5.3 2.0 - - + -
270A ILE* 5.8 0.6 - - - +
292A GLY 3.3 21.5 - - - +
293A GLY* 3.7 11.5 + - - +
294A GLY 3.5 1.6 + - - -
295A ILE 3.3 0.2 - - - -
296A THR* 1.3 79.1 - - - +
298A MET* 1.3 67.0 + - - +
300A ARG* 3.0 22.0 + - - +
301A VAL* 3.1 17.6 + - + +
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Residues in contact with MET 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ILE* 5.4 4.9 - - + -
287A MET* 3.2 52.9 - - + +
288A PRO 4.2 10.1 - - - +
289A LEU* 3.8 23.3 - - + -
292A GLY* 3.5 20.0 - - - +
294A GLY 3.0 22.3 + - - +
297A ALA* 1.3 73.8 - - - +
299A ARG* 1.3 60.9 + - - +
301A VAL* 3.3 28.2 + - + +
302A ALA* 2.9 33.6 + - + +
312A THR* 6.4 0.9 - - + -
314A PHE* 4.2 9.2 - - + -
331A PHE* 3.6 10.4 - - + -
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Residues in contact with ARG 299 (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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96A TRP* 4.6 17.3 - - - -
110A LEU 4.8 2.8 + - - -
111A LEU* 2.8 53.4 + - - +
295A ILE* 3.0 20.3 + - + +
296A THR* 3.9 7.6 - - - +
298A MET* 1.3 75.9 - - - +
300A ARG* 1.3 61.0 + - + +
302A ALA* 3.4 1.4 + - - +
303A ASP* 3.0 47.0 + - - +
331A PHE* 3.6 16.2 - - + -
334A TRP* 3.9 23.1 - - + -
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Residues in contact with ARG 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLU* 2.9 41.1 + - - -
69A TRP* 5.1 4.4 - - - -
70A GLN* 4.1 8.9 - - - +
270A ILE* 4.0 13.8 - - + +
296A THR* 3.3 32.2 + - - +
297A ALA* 3.0 11.7 + - - +
299A ARG* 1.3 80.6 - - + +
301A VAL* 1.3 55.7 + - - +
303A ASP* 3.9 6.0 - - - +
304A LEU* 3.1 28.9 + - - +
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Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ILE* 3.9 32.1 - - + +
273A CYS* 4.3 8.3 - - - -
277A ILE* 4.4 4.5 - - + +
285A ILE* 4.1 26.7 - - + -
287A MET* 3.8 23.6 - - + -
297A ALA* 3.1 15.1 + - + +
298A MET* 3.3 26.9 + - + +
300A ARG* 1.3 73.5 - - - +
302A ALA* 1.3 59.0 + - - +
304A LEU* 3.3 4.0 + - - +
305A ALA* 2.9 27.5 + - - +
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Residues in contact with ALA 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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285A ILE* 5.4 1.1 - - - -
298A MET* 2.9 18.7 + - + +
299A ARG* 3.8 3.6 - - - +
301A VAL* 1.3 77.9 - - - +
303A ASP* 1.3 59.9 + - - +
305A ALA* 3.3 6.0 + - - -
306A SER* 2.9 24.6 + - - -
312A THR* 3.9 18.2 - - + -
331A PHE* 3.9 7.9 - - + -
334A TRP* 5.5 0.2 - - + -
335A VAL* 3.8 27.6 - - + -
337A ASN* 2.9 13.6 + - - +
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Residues in contact with ASP 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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299A ARG* 3.0 37.7 + - - +
300A ARG* 3.9 6.8 + - - +
302A ALA* 1.3 75.9 - - - +
304A LEU* 1.3 64.9 + - - +
306A SER* 2.7 25.6 + - - -
307A LEU* 3.5 8.7 + - - +
334A TRP* 4.2 17.7 - - - -
335A VAL* 5.4 0.2 - - - +
336A PRO* 5.3 5.2 - - - +
337A ASN* 5.2 2.3 - - - +
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Residues in contact with LEU 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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270A ILE* 4.1 22.4 - - + -
274A ARG* 4.1 35.7 - - + +
277A ILE* 4.0 15.9 - - + -
278A GLN* 4.1 24.0 - - + +
300A ARG 3.1 17.6 + - - +
301A VAL 3.3 4.9 + - - +
303A ASP* 1.3 74.6 - - - +
305A ALA* 1.3 65.4 + - - +
307A LEU* 3.2 31.8 + - + +
308A TYR* 3.5 14.1 - - + -
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Residues in contact with ALA 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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277A ILE* 3.7 19.5 - - + +
285A ILE* 4.4 8.7 - - + -
301A VAL 2.9 13.3 + - - +
302A ALA* 3.4 12.1 - - - +
304A LEU* 1.3 77.7 - - - +
306A SER* 1.3 56.9 + - - +
308A TYR* 2.9 18.4 + - - -
310A VAL* 3.0 49.8 + - + +
337A ASN* 3.8 2.7 - - - +
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Residues in contact with SER 306 (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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302A ALA 2.9 13.7 + - - -
303A ASP* 2.7 23.3 + - - -
304A LEU 3.2 0.4 - - - -
305A ALA* 1.3 76.2 - - - +
307A LEU* 1.3 63.6 + - - +
308A TYR 3.0 0.7 + - - -
309A HIS* 3.4 12.7 + - - +
310A VAL 4.1 2.7 - - - -
336A PRO* 6.0 3.8 - - - -
337A ASN* 3.7 25.4 - - - +
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Residues in contact with LEU 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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303A ASP 4.1 8.1 - - - +
304A LEU* 3.2 26.8 + - + +
306A SER* 1.3 83.0 + - - +
308A TYR* 1.3 80.7 + - + +
309A HIS* 3.6 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
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Atomic class I II III IV V VI VII VIII
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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