Contacts of the strand formed by residues 3 - 9 (chain A) in PDB entry 1XYY
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 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ALA* 1.3 77.8 - - - +
4A ALA* 1.3 60.4 + - - +
31A TYR* 4.4 1.8 - - - -
32A GLU* 3.1 33.9 - - + +
49A GLY* 2.4 38.9 + - - +
50A PHE* 3.9 12.8 - - + -
51A ASP* 2.7 44.7 + - - +
52A LEU* 3.2 7.1 + - - +
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Residues in contact with ALA 4 (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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2A ALA 4.2 0.2 - - - -
3A LYS* 1.3 74.8 - - - +
5A LEU* 1.3 59.2 + - - +
6A ILE* 5.2 1.3 - - + -
26A LEU* 3.8 29.4 - - + -
31A TYR* 3.9 15.0 - - + -
32A GLU 2.6 10.5 + - - +
33A VAL* 3.3 8.4 - - + +
34A ASP* 2.6 36.6 + - - +
50A PHE* 3.8 3.3 - - - -
52A LEU* 3.4 13.2 - - + +
54A LEU* 5.6 0.7 - - + -
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Residues in contact with LEU 5 (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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4A ALA* 1.3 75.3 - - - +
6A ILE* 1.3 65.7 + - - +
7A VAL* 3.8 27.4 - - + -
34A ASP 3.2 14.4 - - - +
36A ARG* 3.9 28.5 - - + +
46A LEU* 3.5 28.3 - - + +
47A PHE* 3.7 22.0 - - + -
50A PHE* 3.5 30.9 - - + -
52A LEU 3.0 7.2 + - - +
53A VAL* 3.4 8.0 - - + -
54A LEU* 3.0 26.5 + - - +
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Residues in contact with ILE 6 (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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4A ALA* 5.2 1.6 - - + +
5A LEU* 1.3 78.4 - - - +
7A VAL* 1.3 65.6 + - - +
8A TYR* 4.4 0.8 - - + -
19A ALA* 3.7 31.2 - - + +
22A ILE* 4.2 9.0 - - + -
23A ALA* 3.5 41.7 - - + +
26A LEU* 4.3 9.9 - - + -
33A VAL* 5.0 6.1 - - + -
34A ASP 2.9 7.2 + - - +
35A SER* 3.4 14.3 + - - +
36A ARG 2.8 27.0 + - - +
54A LEU* 3.4 21.5 - - + +
91A PHE* 3.9 17.0 - - + -
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Residues in contact with VAL 7 (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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5A LEU* 3.8 29.8 - - + -
6A ILE* 1.3 78.8 - - - +
8A TYR* 1.3 62.7 + - - +
36A ARG* 3.1 11.7 - - + +
38A ALA* 3.8 19.7 - - + -
41A VAL* 4.3 10.1 - - + -
46A LEU* 4.4 14.4 - - + -
54A LEU 3.2 6.3 + - - +
55A LEU* 3.3 18.4 - - + +
56A GLY 2.9 26.4 + - - +
71A PHE* 4.4 3.4 - - + -
74A LEU* 3.6 25.8 - - + -
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Residues in contact with TYR 8 (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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6A ILE* 4.4 2.7 - - + -
7A VAL* 1.3 76.7 - - - +
9A GLY* 1.3 57.6 + - - +
10A SER* 4.2 8.1 - - - -
15A THR* 4.3 12.1 - - + -
16A GLU* 3.2 49.8 + - + -
19A ALA* 3.7 30.1 - - + -
20A GLU* 6.2 1.1 - - + -
35A SER* 3.5 23.1 + - - -
36A ARG* 3.3 6.6 + - - -
37A ASP* 3.5 47.9 + - - +
38A ALA* 2.6 32.6 + - - -
56A GLY 3.3 6.7 - - - +
91A PHE* 4.7 0.9 - - + -
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Residues in contact with GLY 9 (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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8A TYR* 1.3 70.3 - - - +
10A SER* 1.3 62.1 + - - -
15A THR* 3.8 4.4 - - - -
37A ASP* 5.1 0.2 - - - -
38A ALA* 4.2 8.5 - - - -
56A GLY 2.8 12.9 + - - -
57A CYS* 3.5 2.6 - - - -
58A SER 3.4 24.6 + - - -
68A GLN* 3.2 26.8 - - - +
70A ASP* 5.0 1.6 - - - -
71A PHE* 4.1 7.5 - - - -
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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