Contacts of the strand formed by residues 17 - 23 (chain A) in PDB entry 2XWB
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 GLU 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A SER* 1.3 75.4 - - - +
18A GLU* 1.3 65.0 + - - +
19A THR* 3.8 4.7 + - - -
65A THR* 3.8 24.6 + - + +
66A PHE 3.2 7.2 - - - +
67A THR* 3.1 22.6 + - + +
133A LYS* 6.2 0.3 - - - +
477A ARG* 5.8 5.2 - - - +
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Residues in contact with GLU 18 (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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9A PRO* 3.5 22.4 - - + +
11A ILE 4.2 2.0 - - - +
12A LEU* 3.7 32.0 - - + -
13A ARG* 3.1 57.2 + - - +
16A SER* 3.8 5.7 + - - +
17A GLU* 1.3 73.6 - - - +
19A THR* 1.3 66.1 + - - +
65A THR* 3.6 2.2 - - - -
66A PHE* 3.2 45.5 + - + -
68A ILE* 5.7 1.3 - - + -
476A GLY 4.4 6.8 - - - +
477A ARG* 4.8 8.3 - - - +
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Residues in contact with THR 19 (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 THR* 4.2 3.8 - - - +
9A PRO* 3.9 12.7 - - - +
17A GLU 3.8 4.4 + - - -
18A GLU* 1.3 78.0 + - - +
20A MET* 1.3 68.4 + - - +
21A VAL* 4.9 5.2 - - + -
63A ASN* 3.5 24.5 - - - +
64A VAL 4.5 0.2 - - - +
65A THR* 3.9 17.6 - - + +
66A PHE* 4.8 0.7 - - - -
477A ARG* 5.8 1.5 - - - +
478A LEU* 3.4 57.3 + - + +
481A ALA* 6.4 0.2 - - + -
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Residues in contact with MET 20 (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* 3.4 37.0 - - + -
7A ILE 3.8 3.1 - - - -
8A THR* 3.6 10.1 - - + -
19A THR* 1.3 78.5 - - - +
21A VAL* 1.3 61.4 + - - +
22A LEU* 5.1 0.2 - - + -
35A VAL* 3.5 36.3 - - + -
62A GLY 3.6 3.8 - - - +
63A ASN* 4.5 0.9 - - - -
64A VAL* 3.0 46.3 + - + +
66A PHE* 4.0 20.6 - - + -
86A VAL* 3.5 28.7 - - + -
87A GLN 4.6 0.4 - - - +
88A ALA* 4.2 13.7 - - + -
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Residues in contact with VAL 21 (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* 3.0 21.5 - - - +
7A ILE* 3.2 30.8 + - + +
19A THR* 4.9 5.6 - - + -
20A MET* 1.3 72.3 - - - +
22A LEU* 1.3 65.0 + - - +
23A GLU* 4.0 27.0 - - + +
61A MET* 5.2 8.5 - - + -
62A GLY 4.0 6.5 - - - +
63A ASN* 5.9 0.7 - - - +
469A THR* 5.5 2.0 - - + -
471A LEU* 4.3 9.0 - - + -
478A LEU* 4.0 21.1 - - + -
481A ALA* 3.7 31.0 - - + -
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Residues in contact with LEU 22 (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 SER 4.3 0.7 - - - -
6A ILE* 3.5 23.6 - - + -
21A VAL* 1.3 74.1 - - - +
23A GLU* 1.3 68.9 - - - +
33A VAL* 3.6 20.0 - - + -
35A VAL* 4.2 5.6 - - + -
52A THR* 3.6 31.2 - - + -
54A LEU* 4.3 13.7 - - + -
60A HIS 4.2 0.2 - - - -
61A MET* 3.3 6.2 - - - +
62A GLY* 3.2 28.6 + - - +
64A VAL* 3.8 22.9 - - + -
88A ALA* 4.4 8.1 - - + -
90A PHE* 3.6 29.4 - - + -
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Residues in contact with GLU 23 (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 TYR* 3.9 1.2 - - - -
5A SER* 3.5 31.5 + - - +
7A ILE* 3.9 13.0 - - - +
21A VAL* 4.0 11.2 + - + +
22A LEU* 1.3 80.5 - - - +
24A ALA* 1.3 65.0 + - - +
25A HIS* 3.5 13.9 - - - +
54A LEU* 4.1 3.6 - - - -
60A HIS 3.4 8.1 - - - +
61A MET* 4.1 7.6 - - + -
90A PHE* 3.7 14.2 - - - -
469A THR* 3.2 24.4 + - - +
483A ARG* 2.9 27.3 + - - +
512A TYR* 2.7 34.1 + - - -
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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