Contacts of the helix formed by residues 277 - 293 (chain A) in PDB entry 5EAA
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 SER 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A ASP 3.3 18.0 + - - -
98A LYS* 3.5 37.3 + - - +
276A ASP* 1.3 74.3 - - - +
278A GLU* 1.3 65.2 + - - +
279A THR 2.9 2.1 + - - -
280A VAL* 3.0 4.2 - - - +
281A ASP* 3.0 28.0 + - - -
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Residues in contact with GLU 278 (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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276A ASP* 3.5 8.7 + - - +
277A SER* 1.3 77.5 - - - +
279A THR* 1.3 59.4 + - - +
281A ASP* 3.7 7.8 - - - +
282A ARG* 2.8 69.3 + - - +
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Residues in contact with THR 279 (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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249A GLU* 5.3 6.3 - - - +
274A ALA* 3.8 15.9 - - + -
275A ALA* 4.6 5.6 + - + +
276A ASP* 2.7 31.0 + - - -
277A SER 2.9 1.0 + - - -
278A GLU* 1.3 76.3 + - - +
280A VAL* 1.3 65.8 + - - +
281A ASP 3.0 1.3 - - - -
282A ARG* 3.3 24.7 + - - +
283A ALA* 2.9 27.3 + - + +
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Residues in contact with VAL 280 (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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98A LYS 3.6 20.9 - - - +
99A ARG 3.8 12.6 - - - +
101A ARG* 3.5 24.5 - - + +
272A LEU* 3.3 34.3 - - + +
274A ALA* 3.3 18.0 - - + +
276A ASP 3.0 10.6 + - - +
277A SER 3.0 18.4 - - - +
279A THR* 1.3 75.0 - - - +
281A ASP* 1.3 62.9 + - - +
283A ALA* 3.6 3.3 - - - +
284A PHE* 2.6 37.3 + - - +
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Residues in contact with ASP 281 (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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98A LYS* 4.5 16.0 + - - +
101A ARG* 3.7 16.4 - - - -
277A SER* 3.0 19.0 + - - +
278A GLU* 3.7 8.3 - - - +
279A THR 3.0 0.2 - - - -
280A VAL* 1.3 87.7 - - - +
282A ARG* 1.3 66.8 + - - +
284A PHE* 2.9 16.8 + - - +
285A SER* 3.0 14.8 + - - -
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Residues in contact with ARG 282 (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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278A GLU* 2.8 52.2 + - - +
279A THR* 3.9 27.3 + - - +
281A ASP* 1.3 77.4 - - - +
283A ALA* 1.3 62.2 + - - +
285A SER* 2.8 25.8 + - - +
286A GLN* 3.7 7.3 + - - +
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Residues in contact with ALA 283 (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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118A PHE* 3.6 23.1 - - + -
272A LEU* 3.9 16.2 - - + -
274A ALA* 5.6 2.7 - - + -
279A THR* 2.9 21.8 + - + +
280A VAL* 3.9 3.8 - - - +
282A ARG* 1.3 75.5 - - - +
284A PHE* 1.3 65.3 + - - +
286A GLN* 3.1 13.3 + - - +
287A MET* 3.2 8.3 + - - +
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Residues in contact with PHE 284 (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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74A ASP* 3.7 22.0 - - + -
101A ARG* 3.5 55.6 - - + -
102A THR 3.5 27.8 - - - -
103A ALA* 3.9 17.9 - - + -
270A CYS 5.0 0.4 - - - -
272A LEU* 3.8 12.3 - - + +
280A VAL 2.6 25.8 + - - +
281A ASP* 2.9 6.5 + - - +
283A ALA* 1.3 72.5 - - - +
285A SER* 1.3 56.3 + - - +
287A MET* 2.8 37.6 + - + +
288A LYS* 2.8 33.6 + - + +
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Residues in contact with SER 285 (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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281A ASP 3.0 11.1 + - - -
282A ARG* 2.8 23.0 + - - +
284A PHE* 1.3 76.5 - - - +
286A GLN* 1.3 62.1 + - - +
288A LYS* 3.3 17.5 + - - +
289A ALA* 3.1 24.4 + - - +
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Residues in contact with GLN 286 (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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118A PHE* 4.2 6.1 - - + -
121A LYS* 3.0 37.9 + - - -
122A ASN* 3.3 36.4 + - + +
282A ARG 3.7 8.9 + - - +
283A ALA* 3.1 11.6 + - - +
285A SER* 1.3 81.4 + - - +
287A MET* 1.3 65.9 + - - +
289A ALA* 3.3 10.0 + - - +
290A ALA* 3.2 8.0 + - - +
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Residues in contact with MET 287 (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 ALA* 5.0 1.6 - - - -
114A VAL* 3.9 15.7 - - + +
115A ALA* 4.1 9.6 - - + -
118A PHE* 3.7 44.1 - - + -
251A ILE* 5.6 1.8 - - + -
270A CYS* 3.9 34.1 - - - +
272A LEU* 4.5 19.3 - - + -
283A ALA 3.2 8.2 + - - +
284A PHE* 2.8 34.6 + - + +
286A GLN* 1.3 74.3 - - - +
288A LYS* 1.3 64.3 + - - +
290A ALA* 3.1 14.8 + - - +
291A ILE* 3.1 19.9 + - + +
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Residues in contact with LYS 288 (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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73A ILE* 3.8 28.3 - - + +
74A ASP* 4.3 26.2 + - + +
101A ARG* 5.8 0.6 - - - +
284A PHE* 2.8 43.5 + - + +
285A SER* 3.4 19.5 - - - +
287A MET* 1.3 75.9 - - - +
289A ALA* 1.3 56.4 + - - +
291A ILE* 3.2 13.3 + - + +
292A ARG* 2.9 29.7 + - - +
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Residues in contact with ALA 289 (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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121A LYS* 4.5 7.5 - - - +
285A SER 3.1 13.6 + - - +
286A GLN* 3.5 21.3 - - - +
287A MET 3.2 0.2 - - - -
288A LYS* 1.3 78.0 - - - +
290A ALA* 1.3 59.8 + - - +
292A ARG* 3.6 9.9 - - - +
293A ALA* 3.3 22.0 + - - +
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Residues in contact with ALA 290 (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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114A VAL* 4.5 10.8 - - + +
117A ASP* 4.4 24.1 - - + +
118A PHE* 4.5 7.9 - - - +
121A LYS* 3.9 15.5 - - + +
286A GLN 3.2 10.5 + - - +
287A MET* 3.1 15.1 + - - +
289A ALA* 1.3 73.5 - - - +
291A ILE* 1.3 65.2 + - - +
293A ALA* 3.2 13.4 + - - +
294A ASN* 3.2 13.9 + - - +
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Residues in contact with ILE 291 (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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73A ILE* 3.3 29.6 - - + +
103A ALA* 4.0 27.6 - - + -
104A GLN 5.3 0.2 - - - +
105A THR* 5.4 0.4 - - - +
114A VAL* 3.7 22.7 - - + -
287A MET* 3.1 17.9 + - + +
288A LYS* 3.4 15.0 - - + +
290A ALA* 1.3 75.1 - - - +
292A ARG* 1.3 56.9 + - - +
294A ASN* 2.7 26.5 + - - -
295A TYR* 3.0 54.3 + - + +
296A SER 3.2 6.8 + - - +
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Residues in contact with ARG 292 (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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73A ILE* 4.0 24.3 - - + +
288A LYS 2.9 17.2 + - - +
289A ALA* 3.6 11.9 - - - +
291A ILE* 1.3 78.8 - - - +
293A ALA* 1.3 57.0 + - - +
294A ASN 3.2 1.1 + - - -
296A SER* 3.0 43.7 + - - +
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Residues in contact with ALA 293 (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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289A ALA 3.3 13.1 + - - +
290A ALA* 3.2 7.4 + - - +
291A ILE 3.1 1.0 - - - -
292A ARG* 1.3 78.0 - - + +
294A ASN* 1.3 62.5 + - - +
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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