Contacts of the strand formed by residues 73 - 79 (chain E) in PDB entry 1XIW
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 73 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40E HIS* 4.2 0.9 - - - -
41E ASN* 3.7 9.6 - - - -
72E SER* 1.3 77.3 - - - +
74E TYR* 1.3 61.8 + - - -
75E TYR* 3.6 9.4 - - - -
91E LEU 3.4 1.6 - - - +
92E TYR* 3.9 20.3 - - - -
93E LEU 2.7 38.3 + - - -
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Residues in contact with TYR 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E GLN 3.8 0.2 - - - +
40E HIS* 3.2 7.3 - - - -
41E ASN* 2.8 45.4 + - - +
73E GLY* 1.3 71.9 - - - -
75E TYR* 1.3 60.5 - - - +
90E TYR* 4.2 18.8 - - + -
91E LEU 3.2 7.4 - - - +
92E TYR* 3.5 35.4 - + + -
2F LYS* 3.6 47.3 - - + +
3F ILE 2.7 30.7 + - - -
4F PRO* 3.2 5.5 - - - +
5F ILE* 3.0 22.1 + - + +
65F VAL* 4.6 4.7 - - + -
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Residues in contact with TYR 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E TYR* 3.7 2.2 + - - -
26E LEU* 3.7 24.0 - - + -
38E TRP* 4.6 6.7 - + + -
39E GLN 3.3 7.9 - - - -
40E HIS* 3.4 37.8 + + + -
45E ILE* 3.9 11.9 - - + -
61E LEU* 4.0 11.0 - - + -
63E LEU* 3.4 29.7 - - + +
71E GLN* 2.6 38.8 + - - +
73E GLY 3.6 14.4 - - - -
74E TYR* 1.3 74.5 - - - +
76E VAL* 1.3 62.1 + - - +
90E TYR* 3.6 2.7 - - - -
91E LEU* 2.8 42.3 + - + +
93E LEU* 3.8 20.6 - - + -
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Residues in contact with VAL 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E TYR* 3.3 3.6 - - - +
38E TRP* 3.2 9.8 - - - -
39E GLN* 3.0 51.7 + - + +
75E TYR* 1.3 76.3 - - - +
77E CYS* 1.3 66.0 + - - +
78E TYR* 4.7 5.7 - - + -
84E PRO* 5.5 2.0 - - + +
87E ALA* 3.4 33.0 - - + -
89E PHE 3.6 19.3 - - - +
90E TYR* 3.6 28.7 - - + +
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Residues in contact with CYS 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E TYR* 3.2 28.2 + - - -
28E CYS* 2.0 52.7 - - + -
30E GLN* 4.0 7.9 - - - +
31E TYR* 4.1 9.0 + - - -
36E ILE* 3.7 11.2 - - + -
37E LEU 3.2 5.8 - - - +
38E TRP* 3.9 12.3 - - + -
76E VAL* 1.3 82.8 - - - +
78E TYR* 1.3 65.6 + - - +
87E ALA* 4.7 1.9 - - - +
89E PHE 5.1 0.2 - - - +
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Residues in contact with TYR 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E TYR* 4.1 7.4 - - - +
36E ILE* 3.6 3.0 - - - -
37E LEU* 2.8 73.9 + - + +
38E TRP 4.3 2.5 - - - -
39E GLN* 4.5 10.1 - - + -
44E ASN* 4.5 1.2 + - - -
76E VAL* 4.7 7.0 - - + -
77E CYS* 1.3 80.6 - - - +
79E PRO* 1.3 81.7 - - + +
82E SER* 3.6 28.5 - - - -
83E LYS 4.4 1.6 - - - +
84E PRO* 3.5 37.2 - - + +
87E ALA* 4.7 12.3 - - + -
102H TYR* 3.7 10.4 - - - +
103H GLY* 2.9 24.6 + - - -
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Residues in contact with PRO 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E TYR* 3.7 41.9 - - + +
34E SER* 3.7 25.6 - - - +
35E GLU 3.4 6.1 - - - +
36E ILE* 4.2 1.8 - - + -
78E TYR* 1.3 95.6 - - + +
80E ARG* 1.3 69.6 + - - +
82E SER* 2.9 39.5 + - - +
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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