Contacts of the strand formed by residues 64 - 72 (chain B) in PDB entry 3NX4
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 ASP 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B SER* 2.8 21.6 + - - +
38B SER* 2.9 18.3 + - - +
40B ASN* 2.7 27.9 + - - +
43B ASP* 5.0 0.2 + - - -
62B GLY* 3.2 1.0 - - - +
63B ILE* 1.3 84.0 - - - +
65B PHE* 1.3 69.0 - - - +
85B LEU 3.3 4.9 - - - +
86B THR* 3.3 11.8 - - - -
97B GLY* 3.3 7.6 - - - -
122B MSE 3.5 15.5 - - - -
125B GLY* 3.3 2.4 - - - -
126B THR* 2.6 41.1 + - - -
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Residues in contact with PHE 65 (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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32B VAL* 3.9 25.1 - - + -
34B VAL* 3.8 25.8 - - + -
36B TRP 3.4 12.6 - - - +
64B ASP* 1.3 76.2 - - - +
66B ALA* 1.3 64.7 + - - +
83B VAL* 5.1 1.1 - - + -
84B LEU* 3.3 2.2 - - - -
85B LEU* 2.8 77.6 + - + +
90B VAL* 4.4 6.1 - - + -
97B GLY* 3.7 22.9 - - - +
102B ALA* 3.8 21.3 - - + -
104B VAL* 4.1 16.2 - - + -
109B LEU* 4.1 12.3 - - + -
122B MSE 3.4 9.6 - - - +
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 3.8 0.9 - - - -
35B HIS* 2.9 21.8 + - - +
36B TRP* 2.9 16.6 + - + +
65B PHE* 1.3 79.6 - - - +
67B GLY* 1.3 59.2 + - - +
83B VAL 3.5 11.2 - - - +
84B LEU* 4.1 5.4 - - + +
112B LEU* 5.8 0.4 - - + -
118B SER* 3.4 34.9 + - - +
121B ALA* 4.7 1.6 - - + -
122B MSE 3.7 17.9 - - + -
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Residues in contact with GLY 67 (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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32B VAL* 3.9 11.6 - - - +
33B ASP 3.3 13.7 - - - -
35B HIS* 3.9 11.0 - - - -
66B ALA* 1.3 76.4 - - - +
68B THR* 1.3 64.7 + - - -
82B GLU* 3.2 9.4 - - - +
83B VAL* 2.9 31.2 + - - +
118B SER* 4.1 1.5 + - - -
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Residues in contact with THR 68 (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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32B VAL* 3.5 3.9 - - - +
33B ASP* 2.8 38.4 + - - +
35B HIS* 3.3 26.0 + - + -
67B GLY* 1.3 74.1 - - - -
69B VAL* 1.3 64.4 + - - +
80B GLY* 4.0 15.7 - - - +
81B GLN 3.3 5.4 - - - -
82B GLU* 3.3 38.1 - - + +
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Residues in contact with VAL 69 (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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30B VAL* 4.0 14.1 - - + -
31B THR 3.6 6.7 - - - +
32B VAL* 4.4 1.8 - - - +
33B ASP* 5.1 0.4 - - - +
68B THR* 1.3 71.8 + - - +
70B HIS* 1.3 61.5 + - - +
71B ALA 3.6 27.8 - - - +
72B SER* 3.9 8.1 - - - -
77B PHE* 4.5 6.7 - - + -
78B HIS 3.3 31.2 - - - +
79B ALA* 3.6 1.5 - - - -
80B GLY* 2.7 26.2 + - - -
81B GLN* 2.9 21.3 + - + +
83B VAL* 3.7 27.8 - - + -
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Residues in contact with HIS 70 (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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31B THR* 2.7 29.5 + - + +
33B ASP* 3.1 32.1 + - - +
68B THR 3.3 2.0 + - - -
69B VAL* 1.3 73.7 - - - +
71B ALA* 1.3 67.2 + - + +
79B ALA* 3.8 14.0 - - - +
101B ARG* 3.4 35.2 + - - -
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Residues in contact with ALA 71 (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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29B ASP 4.6 0.4 - - - -
30B VAL* 3.4 1.3 - - - -
31B THR* 2.8 39.6 + - - +
69B VAL* 3.6 5.1 - - - +
70B HIS* 1.3 91.6 - - + +
72B SER* 1.3 63.4 + - - +
73B GLU* 5.6 3.8 - - - +
79B ALA* 5.0 4.0 - - - -
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Residues in contact with SER 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASP 3.4 5.4 - - - -
30B VAL* 3.8 7.0 - - - +
69B VAL* 3.9 14.3 - - - +
71B ALA* 1.3 77.5 - - - +
73B GLU* 1.3 71.4 + - - +
74B ASP* 2.9 33.9 + - - +
77B PHE* 3.0 21.2 + - - +
78B HIS* 4.8 2.7 - - - -
79B ALA* 5.0 1.6 - - - +
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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