Contacts of the strand formed by residues 30 - 39 (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 VAL 30 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B GLY 3.3 0.4 - - - -
29B ASP* 1.3 87.3 - - - +
31B THR* 1.3 66.9 + - - +
32B VAL* 4.1 5.6 + - + -
69B VAL* 4.0 21.1 - - + -
71B ALA 3.4 10.1 - - - +
72B SER* 3.8 13.5 - - - +
74B ASP* 3.9 7.2 - - + -
77B PHE* 4.6 4.3 - - + -
102B ALA 4.0 0.3 - - - +
103B ARG* 3.4 3.8 - - - -
104B VAL* 2.9 34.4 + - - +
106B GLY* 3.6 27.8 - - - -
109B LEU* 3.5 27.1 - - + -
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Residues in contact with THR 31 (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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25B LEU* 5.2 2.2 - - + -
28B GLY 5.0 0.7 + - - -
29B ASP 5.6 0.2 - - - -
30B VAL* 1.3 73.1 - - - +
32B VAL* 1.3 58.3 + - - +
69B VAL* 3.6 4.2 - - - +
70B HIS* 2.7 43.7 + - + -
71B ALA* 2.8 26.0 + - - +
101B ARG* 3.7 31.2 - - + +
102B ALA 3.4 9.4 - - - +
103B ARG* 3.6 24.0 + - + +
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Residues in contact with VAL 32 (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* 4.1 16.8 - - + +
31B THR* 1.3 79.3 - - - +
33B ASP* 1.3 74.4 + - - +
34B VAL* 3.4 3.7 + - + +
65B PHE* 3.9 32.5 - - + -
67B GLY* 3.9 9.2 - - - -
68B THR 3.5 19.1 - - - +
69B VAL* 4.6 2.7 - - - -
83B VAL* 4.0 20.4 - - + -
101B ARG* 3.3 7.8 - - - +
102B ALA 2.7 38.1 + - - +
104B VAL* 5.0 1.8 - - + -
109B LEU* 4.4 5.6 - - + -
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Residues in contact with ASP 33 (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 4.3 0.2 - - - -
32B VAL* 1.3 69.4 - - - +
34B VAL* 1.3 62.7 + - - +
35B HIS* 3.6 12.1 + - + +
67B GLY* 3.3 3.1 - - - -
68B THR* 2.8 44.0 + - - +
69B VAL 5.1 0.2 - - - -
70B HIS* 3.1 29.1 + - - +
100B GLU 3.8 6.6 - - - +
101B ARG* 2.8 36.8 + - - -
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Residues in contact with VAL 34 (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* 3.8 12.8 - - + +
33B ASP* 1.3 72.0 - - - +
35B HIS* 1.3 64.5 + - - +
36B TRP 3.6 23.3 - - - +
65B PHE* 3.8 29.4 - - + -
66B ALA 3.9 4.5 - - - +
67B GLY* 4.3 0.7 - - - -
97B GLY 3.6 14.8 - - - +
99B ALA 3.3 26.0 - - - +
100B GLU 3.0 9.5 + - - +
101B ARG* 4.3 0.4 - - - -
102B ALA* 4.1 16.2 - - + +
323B ILE* 3.6 12.8 - - + +
324B LYS 3.2 18.4 - - - +
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Residues in contact with HIS 35 (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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33B ASP* 3.6 15.1 + - + +
34B VAL* 1.3 82.2 - - - +
36B TRP* 1.3 84.8 + - + +
66B ALA 2.9 8.0 + - - +
67B GLY* 4.0 9.0 - - - -
68B THR* 3.3 36.9 + - + +
82B GLU* 4.8 4.8 + - - -
118B SER* 4.9 2.6 + - - +
322B LYS* 4.6 0.7 - - - +
323B ILE* 2.9 8.7 + - - -
324B LYS* 2.9 39.0 + - - +
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Residues in contact with TRP 36 (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 VAL* 3.6 4.3 - - - +
35B HIS* 1.3 93.1 - - + +
37B SER* 1.3 61.2 + - - +
65B PHE* 3.4 3.3 - - - -
66B ALA 2.9 29.8 + - - +
118B SER* 3.7 24.8 + - - +
119B ARG* 3.7 48.7 - - + +
122B MSE 3.5 20.8 - - + +
297B GLU* 3.5 32.1 - - - -
320B LEU* 3.8 19.3 - - + -
321B VAL 3.5 7.6 - - - -
322B LYS* 3.6 36.3 - - + -
323B ILE* 4.0 4.3 - - - -
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Residues in contact with SER 37 (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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36B TRP* 1.3 75.2 - - - +
38B SER* 1.3 73.4 + - - +
62B GLY* 4.7 1.2 - - - -
64B ASP* 2.8 24.4 + - - +
97B GLY 3.9 13.9 - - - -
98B LEU* 3.5 31.1 - - - +
122B MSE 3.7 9.0 - - - +
320B LEU* 3.6 10.7 - - - +
321B VAL* 2.9 26.7 + - - +
323B ILE* 3.8 6.7 - - - +
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Residues in contact with SER 38 (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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37B SER* 1.3 86.7 + - - +
39B LEU* 1.3 73.9 + - - +
40B ASN* 3.4 4.4 + - - -
43B ASP* 3.5 9.7 - - - +
62B GLY* 5.1 0.7 - - - -
64B ASP* 2.9 29.6 + - - +
98B LEU* 4.2 2.9 - - - +
122B MSE 3.5 12.8 - - - -
318B ARG* 3.0 23.0 + - - -
319B THR 3.2 16.2 - - - -
320B LEU* 4.4 0.2 - - - -
321B VAL* 4.0 5.4 - - - -
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Residues in contact with LEU 39 (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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38B SER* 1.3 83.1 - - - +
40B ASN* 1.3 64.4 + - - +
43B ASP* 3.7 5.8 - - + -
44B ALA* 5.5 0.4 - - - +
47B ILE* 4.0 11.9 - - + -
98B LEU* 3.9 24.2 - - + -
298B ILE* 4.3 3.4 - - + -
303B ALA* 3.5 36.8 - - + +
306B PHE* 4.0 11.2 - - + -
307B ALA* 3.9 16.4 - - + +
310B ILE* 3.8 21.5 - - + +
318B ARG* 3.3 15.3 + - - -
319B THR* 2.9 22.8 + - + +
321B VAL* 3.9 14.8 - - + -
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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