Contacts of the strand formed by residues 30 - 39 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A GLY 3.4 0.4 - - - -
29A ASP* 1.3 84.2 - - - +
31A THR* 1.3 63.1 + - - +
32A VAL* 4.0 6.1 + - + +
69A VAL* 4.0 24.9 - - + -
71A ALA 3.7 8.5 - - - +
72A SER* 3.9 14.1 - - - +
74A ASP* 3.9 8.3 - - + -
77A PHE* 4.4 4.9 - - + -
102A ALA 3.8 0.7 - - - +
103A ARG* 3.3 4.9 - - - -
104A VAL* 2.9 33.0 + - - +
106A GLY* 3.9 29.8 - - - +
109A LEU* 3.6 26.9 - - + -
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Residues in contact with THR 31 (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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22A GLU* 3.7 23.6 + - - +
25A LEU* 5.4 2.2 - - + -
28A GLY 5.2 0.5 + - - -
29A ASP 4.2 0.6 + - - -
30A VAL* 1.3 71.6 - - - +
32A VAL* 1.3 63.4 + - - +
33A ASP* 4.7 3.1 - - - +
69A VAL* 3.6 3.8 - - - +
70A HIS* 2.8 45.7 + - + -
71A ALA* 2.9 25.2 + - - +
101A ARG* 5.2 4.0 - - + -
102A ALA 3.5 9.0 - - - +
103A ARG* 3.7 25.1 + - - +
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Residues in contact with VAL 32 (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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30A VAL* 4.2 19.5 - - + +
31A THR* 1.3 79.4 - - - +
33A ASP* 1.3 74.5 + - - +
34A VAL* 3.5 2.5 + - + +
65A PHE* 3.8 36.8 - - + -
67A GLY* 3.9 9.6 - - - -
68A THR 3.6 18.8 - - - +
69A VAL* 4.7 2.5 - - + -
83A VAL* 4.1 14.8 - - + -
101A ARG* 3.2 7.3 - - - +
102A ALA* 2.8 40.1 + - + +
104A VAL* 4.9 1.8 - - + -
109A LEU* 4.4 5.2 - - + -
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Residues in contact with ASP 33 (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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31A THR* 4.7 1.0 - - - +
32A VAL* 1.3 72.3 - - - +
34A VAL* 1.3 62.1 + - - +
35A HIS* 3.7 16.6 + - + +
67A GLY* 3.2 2.6 - - - -
68A THR* 2.8 38.5 + - - +
70A HIS* 3.7 32.8 + - - +
100A GLU 3.7 4.5 - - - -
101A ARG* 3.1 37.9 + - - +
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Residues in contact with VAL 34 (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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32A VAL* 4.0 12.3 - - + +
33A ASP* 1.3 70.7 - - - +
35A HIS* 1.3 68.0 + - - +
36A TRP 3.4 23.8 - - - +
65A PHE* 4.0 26.5 - - + -
66A ALA 3.8 4.7 - - - +
67A GLY* 4.2 0.9 - - - -
97A GLY* 3.7 14.8 - - - +
99A ALA 3.2 25.4 - - - +
100A GLU* 2.9 11.9 + - - +
101A ARG 4.2 0.2 - - - -
102A ALA* 4.1 18.2 - - + +
323A ILE* 3.5 21.5 - - + +
324A LYS* 4.0 3.3 + - - -
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Residues in contact with HIS 35 (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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33A ASP* 3.8 15.0 + - + +
34A VAL* 1.3 81.5 - - - +
36A TRP* 1.3 82.4 + - + +
66A ALA 2.9 8.4 + - - +
67A GLY* 3.9 8.8 - - - -
68A THR* 3.1 34.5 + - - -
82A GLU* 4.8 4.8 + - - -
118A SER* 4.7 3.4 + - - +
323A ILE* 3.1 19.9 + - - -
324A LYS* 3.2 44.7 + - + +
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Residues in contact with TRP 36 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A VAL* 3.4 10.8 - - - +
35A HIS* 1.3 86.7 - - + +
37A SER* 1.3 60.0 + - - +
65A PHE* 3.4 0.5 - - - -
66A ALA 2.9 28.5 + - - +
118A SER* 3.5 24.8 - - - +
119A ARG* 3.5 49.3 - - + +
122A MSE 3.6 22.7 - - + -
297A GLU* 3.7 10.3 - - - -
320A LEU* 3.7 32.3 - - + -
321A VAL 3.4 5.4 - - - -
322A LYS* 3.5 57.2 - - + -
323A ILE* 4.2 1.3 - - - -
324A LYS* 3.8 21.7 - - + +
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Residues in contact with SER 37 (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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36A TRP* 1.3 73.6 - - - +
38A SER* 1.3 72.6 + - - +
62A GLY* 4.7 0.9 - - - -
64A ASP* 2.8 20.6 + - - +
97A GLY* 3.5 22.8 + - - -
98A LEU* 3.6 24.8 - - - +
122A MSE 3.7 11.5 - - - +
320A LEU* 3.5 10.4 - - - +
321A VAL* 2.9 27.6 + - - +
323A ILE* 4.0 6.2 - - - +
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Residues in contact with SER 38 (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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37A SER* 1.3 87.5 + - - +
39A LEU* 1.3 71.9 + - - +
40A ASN* 3.4 4.2 + - - -
43A ASP* 3.5 10.9 - - - +
62A GLY* 5.1 1.0 - - - -
64A ASP* 3.0 23.5 + - - +
98A LEU* 4.2 3.1 - - - +
122A MSE 3.4 13.9 - - - -
318A ARG* 2.8 32.5 + - - -
319A THR 3.2 12.6 - - - -
320A LEU* 4.6 0.2 - - - -
321A VAL* 4.0 4.7 - - - -
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Residues in contact with LEU 39 (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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38A SER* 1.3 81.2 - - - +
40A ASN* 1.3 63.5 + - - +
43A ASP* 3.7 6.3 - - + -
44A ALA* 5.7 1.1 - - - +
47A ILE* 4.0 15.0 - - + -
98A LEU* 3.8 28.0 - - + -
298A ILE* 4.0 7.6 - - + -
303A ALA* 3.7 17.5 - - + +
306A PHE* 3.7 30.3 - - + -
307A ALA* 4.2 6.7 - - + +
310A ILE* 3.8 19.6 - - + +
318A ARG* 3.3 14.8 + - - -
319A THR* 3.0 29.1 + - + +
321A VAL* 3.9 9.4 - - + -
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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