Contacts of the strand formed by residues 30 - 36 (chain A) in PDB entry 2E56
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 ALA 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ASN* 3.4 1.1 - - - -
27A SER* 2.8 37.5 + - - +
29A ASP* 1.3 89.2 + - - +
31A SER* 1.3 61.6 + - - +
32A ILE* 4.2 6.5 - - + -
52A ILE* 3.8 10.5 - - + +
54A LEU* 3.7 22.4 - - + -
153A ILE* 4.0 9.2 - - + -
154A LEU 3.2 5.8 - - - +
156A GLN* 3.3 13.7 - - - +
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Residues in contact with SER 31 (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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23A TRP* 3.4 21.8 - - - -
25A CYS 3.9 0.4 - - - -
26A ASN* 2.7 22.3 + - - -
30A ALA* 1.3 74.3 - - - +
32A ILE* 1.3 60.2 + - - +
33A SER* 5.2 0.5 + - - -
152A VAL 3.4 3.8 - - - +
153A ILE* 3.4 0.9 - - - -
154A LEU* 2.8 46.6 + - - +
156A GLN* 3.9 3.4 - - - -
801A NAG 3.2 28.0 + - - -
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Residues in contact with ILE 32 (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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23A TRP* 3.8 6.0 - - - -
24A VAL* 2.9 44.1 + - + -
25A CYS* 3.0 21.6 + - - +
30A ALA* 4.7 1.6 - - + -
31A SER* 1.3 79.6 + - - +
33A SER* 1.3 69.4 + - - +
48A VAL* 5.6 0.4 - - + -
51A CYS* 4.0 16.4 - - - -
52A ILE* 4.0 33.9 - - + +
151A PHE* 4.3 5.8 - - + -
152A VAL 3.6 5.6 - - - +
153A ILE* 4.3 24.7 - - + -
701A MYR 4.3 24.7 - - + -
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Residues in contact with SER 33 (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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21A GLN* 3.8 19.9 + - - -
22A TYR 2.9 16.2 - - - -
23A TRP* 3.8 25.1 - - - +
24A VAL* 4.3 1.6 - - - +
31A SER 4.1 0.5 + - - -
32A ILE* 1.3 75.2 - - - +
34A TYR* 1.3 66.5 + - - +
151A PHE* 3.4 6.8 - - - +
152A VAL* 2.8 45.3 + - - +
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Residues in contact with TYR 34 (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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21A GLN* 4.1 1.8 - - - +
22A TYR* 2.8 69.9 + + + +
23A TRP 5.3 1.1 - - - -
24A VAL* 3.7 28.7 - - + -
33A SER* 1.3 76.5 - - - +
35A THR* 1.3 77.3 + - - +
36A TYR* 3.9 10.7 + + - -
44A ILE* 3.2 25.4 + - + +
45A SER* 4.8 0.3 - - - -
46A ILE* 4.2 20.5 + - + +
149A LEU* 3.8 26.0 - - + -
150A GLU 3.1 18.6 - - - +
151A PHE* 3.6 23.1 - + + -
152A VAL* 4.5 0.9 - - - +
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Residues in contact with THR 35 (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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19A GLN* 4.1 27.7 + - - +
20A LYS 3.6 21.1 - - - +
21A GLN* 3.8 22.7 - - - +
22A TYR* 4.5 1.3 - - - -
34A TYR* 1.3 87.1 - - - +
36A TYR* 1.3 65.8 + - - +
37A CYS* 5.6 0.2 - - - -
149A LEU* 3.7 3.5 - - - -
150A GLU* 3.0 48.0 + - - +
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Residues in contact with TYR 36 (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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19A GLN* 5.3 2.6 - - - +
20A LYS 5.0 0.6 + - - -
22A TYR* 3.3 43.2 - + - -
34A TYR* 3.9 9.4 + + - -
35A THR* 1.3 79.0 + - - +
37A CYS* 1.3 63.2 + - - +
38A ASP 5.0 1.3 - - - +
40A MET* 3.8 36.3 - - + -
41A GLN 5.4 3.8 - - - -
42A TYR 4.1 16.8 - - - -
43A PRO* 3.4 11.4 - - + +
44A ILE* 2.9 38.4 + - + +
147A PHE* 5.8 4.5 - - + -
148A CYS 3.8 6.3 - - - +
149A LEU* 3.5 23.8 - - + -
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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