Contacts of the strand formed by residues 71 - 77 (chain B) in PDB entry 4XCS
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 CYS 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B TYR* 3.2 27.6 - - + -
39B VAL 4.3 0.2 - - - -
40B VAL* 3.6 33.4 - - - -
66B PHE* 2.9 40.1 + - + +
67B LYS* 3.0 21.4 - - - +
69B LEU* 4.0 12.8 - - + +
70B ASN* 1.3 78.6 - - - +
72B GLN* 1.3 61.5 + - - +
160B VAL* 4.2 9.2 - - + -
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Residues in contact with GLN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B TYR* 3.5 44.2 - - + -
37B LYS* 3.6 20.9 - - - +
38B TYR 2.8 12.2 + - - +
39B VAL* 3.1 9.4 - - + +
40B VAL 2.9 22.2 + - - -
67B LYS* 4.1 12.5 - - - +
70B ASN 4.3 0.4 + - - -
71B CYS* 1.3 72.1 - - - +
73B VAL* 1.3 81.9 + - - +
74B ILE* 3.8 12.6 - - + -
101B ASN 5.2 0.9 - - - +
102B ILE* 5.0 2.4 - - - +
103B PRO* 3.4 17.7 - - - +
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B VAL* 3.3 14.8 - - + +
42B PHE* 3.8 25.6 - - + -
59B PHE* 4.1 15.0 - - + +
63B ALA* 5.4 2.7 - - + -
66B PHE* 3.4 50.0 - - + -
67B LYS* 5.4 0.2 - - - +
71B CYS 4.0 0.4 + - - -
72B GLN* 1.3 95.0 + - - +
74B ILE* 1.3 64.1 + - - +
102B ILE* 3.8 26.8 - - + +
103B PRO* 3.5 9.0 - - - +
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Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PHE* 5.7 2.5 - - + -
29B ILE* 4.8 5.6 - - + -
31B LEU* 4.7 9.6 - - + -
34B TYR* 3.8 32.8 - - + +
39B VAL* 4.2 14.6 - - + -
40B VAL 2.9 11.1 + - - +
41B PHE* 3.3 17.4 - - + -
42B PHE* 3.0 29.1 + - - -
72B GLN* 3.8 12.3 - - + -
73B VAL* 1.3 79.5 - - - +
75B GLY* 1.3 71.5 + - - +
102B ILE* 5.2 0.2 - - - -
103B PRO* 3.7 21.3 - - + +
105B VAL* 3.7 22.9 - - + -
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Residues in contact with GLY 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B PHE* 3.4 28.8 - - - -
44B TYR* 4.7 0.2 - - - -
74B ILE* 1.3 78.1 - - - +
76B ALA* 1.3 63.6 + - - +
102B ILE* 4.5 1.6 - - - +
103B PRO 3.1 10.8 + - - -
104B LEU* 3.4 16.0 - - - +
105B VAL 2.8 24.1 + - - -
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 3.6 29.8 - - + -
42B PHE 2.8 11.1 + - - +
43B PHE* 3.2 20.7 - - + -
44B TYR* 2.9 36.4 + - - -
75B GLY* 1.3 75.1 - - - +
77B SER* 1.3 62.7 + - - +
84B HIS* 4.9 0.4 - - - -
105B VAL* 3.5 18.2 - - + +
107B ASP* 6.1 0.2 - - + -
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Residues in contact with SER 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B PHE* 4.0 11.2 - - - -
44B TYR* 3.2 37.7 - - - -
45B PRO 4.0 3.4 - - - -
76B ALA* 1.3 77.5 - - - +
78B VAL* 1.3 61.5 + - - +
79B ASP* 2.6 29.6 + - - +
84B HIS* 3.0 14.1 + - - -
105B VAL 3.4 6.5 + - - +
107B ASP* 3.1 23.4 + - - +
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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