Contacts of the strand formed by residues 31 - 41 (chain A) in PDB entry 1NCO
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 ALA 31 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLY 3.7 1.8 + - - +
30A THR* 1.3 88.6 - - - +
32A TYR* 1.3 60.3 + - - +
54A SER* 6.0 4.0 - - - -
55A VAL 3.2 7.6 - - - +
56A THR* 3.9 13.0 - - - +
99A ASP* 3.6 10.4 - - - +
100A ALA 4.6 1.6 + - - -
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Residues in contact with TYR 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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26A LEU* 3.6 42.9 - - + +
27A GLN* 2.9 35.3 + - - +
30A THR* 3.6 29.4 - - + +
31A ALA* 1.3 74.2 - - - +
33A ASP* 1.3 68.7 + - - +
54A SER* 3.3 7.0 - - - -
55A VAL* 2.7 49.3 + - + +
57A ALA* 4.0 6.7 - - + -
97A LEU* 4.1 12.1 - - + -
98A SER* 3.3 11.4 - - - +
99A ASP* 3.4 33.2 + - + -
103A ASN 4.0 8.5 - - - -
104A GLY* 4.9 3.4 - - - -
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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
----------------------------------------------------------
32A TYR* 1.3 74.9 - - - +
34A VAL* 1.3 60.5 + - - +
52A PHE* 4.3 23.1 - - + +
53A SER 3.6 8.6 - - - +
54A SER* 4.9 4.9 - - - -
96A GLY 3.7 0.3 - - - +
97A LEU* 3.1 25.5 - - - +
98A SER* 2.8 18.4 + - - +
99A ASP 6.1 0.6 - - - -
114A MRD 3.8 15.1 - - + +
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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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21A VAL* 3.9 28.7 - - + -
32A TYR 4.1 1.6 - - - +
33A ASP* 1.3 74.2 - - - +
35A GLY* 1.3 59.6 + - - +
52A PHE* 3.3 6.3 - - - +
53A SER* 2.8 43.4 + - - +
55A VAL* 4.0 14.6 - - + -
65A THR* 3.5 33.4 - - + -
67A LEU* 3.6 11.7 - - + +
95A VAL* 5.0 0.4 - - + -
96A GLY 3.3 11.0 - - - +
97A LEU* 3.4 20.6 - - + -
114A MRD 3.9 1.6 - - - -
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Residues in contact with GLY 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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34A VAL* 1.3 78.1 - - - +
36A GLN* 1.3 60.0 + - - -
52A PHE* 3.6 17.9 - - - -
67A LEU* 3.9 14.6 - - - -
95A VAL* 3.2 3.5 - - - +
96A GLY 3.0 32.4 + - - -
114A MRD 3.3 14.9 - - - +
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Residues in contact with GLN 36 (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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35A GLY* 1.3 73.5 - - - -
37A CYS* 1.3 67.3 + - - +
47A CYS* 3.7 0.3 - - - +
48A ASN* 2.9 40.3 + - + +
52A PHE* 4.1 2.4 - - - -
67A LEU* 4.1 5.9 - - + +
68A THR 4.6 0.6 - - - +
69A VAL* 3.5 7.8 - - - -
70A ARG* 2.8 48.0 + - - +
73A PHE* 3.7 13.8 - - + -
88A CYS* 3.1 22.8 - - - -
93A CYS* 4.0 2.7 - - + +
94A GLN 3.2 12.8 - - - +
95A VAL* 4.0 8.3 - - + -
110A ILE* 3.8 22.9 - - + +
112A PHE* 3.9 1.0 - - - -
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Residues in contact with CYS 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 GLN* 1.3 75.5 - - - +
38A ALA* 1.3 60.3 + - - +
45A LEU* 3.9 16.4 - - + -
46A ALA 3.3 7.0 - - - +
47A CYS* 2.0 47.6 - - - -
52A PHE* 4.5 2.0 - - - -
73A PHE* 4.3 6.1 - - - -
93A CYS* 3.3 3.2 - - - -
94A GLN* 2.8 35.0 + - - +
114A MRD 3.6 37.0 - - + -
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Residues in contact with ALA 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 CYS* 1.3 73.9 - - - +
39A TRP* 1.3 65.4 + - - +
40A VAL* 3.3 8.4 + - + +
45A LEU* 3.4 4.8 - - - -
46A ALA 2.9 33.0 + - - +
86A VAL* 3.6 30.5 - - + -
91A ALA* 4.3 8.7 - - + -
92A ALA 3.6 13.2 - - - +
93A CYS* 4.0 7.6 - - - -
94A GLN* 5.4 0.2 - - - -
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Residues in contact with TRP 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 ALA* 1.3 72.1 - - - +
40A VAL* 1.3 61.9 + - - +
41A ASP 3.2 17.5 - - - +
42A THR* 5.2 0.2 - - - -
43A GLY* 3.5 15.0 - - - +
44A VAL 3.0 36.5 + - - +
45A LEU* 3.6 33.9 - - + +
91A ALA* 5.5 1.7 - - - +
92A ALA* 3.9 19.1 + - + +
94A GLN* 3.9 27.1 - - + +
114A MRD 6.1 0.2 - - + -
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Residues in contact with VAL 40 (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 ALA* 3.7 17.0 - - + +
39A TRP* 1.3 76.7 - - - +
41A ASP* 1.3 59.7 + - + +
44A VAL* 2.8 32.1 + - + +
46A ALA* 3.9 17.0 - - + -
77A LEU* 4.3 0.2 - - + -
83A TRP* 3.6 66.1 + - + +
86A VAL* 4.6 2.9 - - + -
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Residues in contact with ASP 41 (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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39A TRP* 3.2 10.8 - - - +
40A VAL* 1.3 79.8 - - + +
42A THR* 1.4 81.7 + - - +
43A GLY 3.1 1.4 + - - -
44A VAL* 2.8 44.2 + - + +
83A TRP* 5.9 1.1 - - - +
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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