Contacts of the strand formed by residues 84 - 90 (chain A) in PDB entry 1NDM
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 GLY 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLN* 5.9 0.7 - - - -
38A GLN 4.2 4.9 - - - -
39A LYS* 4.5 6.7 - - - -
82A ASP 3.6 2.8 + - - -
83A PHE* 1.3 73.5 - - - +
85A MET* 1.3 59.7 + - - -
86A TYR* 4.1 4.3 - - - -
103A LYS* 3.4 22.9 - - - +
104A LEU* 2.8 37.8 + - - +
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Residues in contact with MET 85 (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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9A ALA 6.0 0.2 - - - +
37A GLN* 3.5 4.0 - - - +
38A GLN* 2.7 49.5 + - + +
84A GLY* 1.3 69.9 - - - -
86A TYR* 1.3 65.0 + - - +
87A PHE* 3.7 38.8 + - + -
100A GLY 4.5 9.2 - - - +
101A GLY* 4.6 6.1 - - - -
102A THR 3.7 2.0 - - - +
103A LYS* 3.5 46.6 - - + +
339B LYS* 5.6 3.1 - - - +
343B ASN* 4.2 25.8 - - + +
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Residues in contact with TYR 86 (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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6A GLN* 3.0 9.0 + - - +
21A LEU* 3.4 25.4 - - + -
35A TRP* 5.0 1.8 - - + -
36A TYR 3.3 6.1 - - - -
37A GLN* 2.6 27.7 + - + -
47A LEU* 3.7 25.8 - - + -
62A PHE* 3.6 16.9 - + - -
73A LEU* 3.5 24.9 - - + -
75A ILE* 4.9 1.8 - - + -
82A ASP* 2.5 32.7 + - - +
84A GLY 3.7 13.5 - - - -
85A MET* 1.3 77.0 - - - +
87A PHE* 1.3 62.3 + - - +
101A GLY* 3.3 1.9 - - - -
102A THR 2.9 35.1 + - - +
104A LEU* 3.5 25.7 - - + +
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Residues in contact with PHE 87 (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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6A GLN* 3.6 4.5 - - - -
34A HIS 3.8 0.3 - - - +
35A TRP* 3.4 6.7 - - - -
36A TYR* 2.7 47.9 + - + +
38A GLN* 3.8 21.5 - - + -
85A MET* 3.7 43.1 - - + -
86A TYR* 1.3 79.0 - - - +
88A CYS* 1.3 62.3 + - - +
98A PHE* 4.6 5.8 - - + -
99A GLY 3.3 21.3 - - - -
100A GLY* 3.7 19.3 - - - -
101A GLY* 3.7 4.9 - - - -
339B LYS* 4.2 2.0 - - - -
343B ASN 3.5 24.7 - - - -
344B LYS* 4.8 1.3 - - - -
345B LEU* 3.7 30.7 - - + -
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Residues in contact with CYS 88 (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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4A LEU* 4.0 2.2 - - - -
6A GLN* 3.3 21.7 + - - -
23A CYS* 2.0 53.4 - - + -
33A LEU* 3.7 12.3 - - + -
34A HIS 3.1 7.9 - - - +
35A TRP* 4.1 8.5 - - + -
36A TYR* 5.1 0.7 - - - -
87A PHE* 1.3 74.8 - - - +
89A GLN* 1.3 61.9 + - - +
98A PHE* 3.4 4.9 - - - +
99A GLY* 2.8 32.7 + - - -
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Residues in contact with GLN 89 (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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4A LEU* 3.6 4.5 - - - -
33A LEU* 3.4 3.6 - - - -
34A HIS* 2.8 39.9 + - - -
36A TYR* 2.7 37.2 + - + -
88A CYS* 1.3 77.9 - - - +
90A GLN* 1.3 83.1 + - - +
91A SER* 4.0 0.4 - - - -
96A TYR* 3.9 13.5 - - + -
97A THR 3.2 20.6 - - - +
98A PHE* 3.6 29.8 - - + -
347B TYR* 4.7 4.8 - - - -
400B MET* 3.0 30.7 - - - +
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Residues in contact with GLN 90 (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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2A ILE* 3.7 29.1 - - + +
4A LEU* 3.5 10.2 - - + +
29A ILE* 3.8 20.4 - - + -
32A ASN 3.2 12.3 - - - +
33A LEU* 4.6 0.2 - - - +
89A GLN* 1.3 84.1 + - - +
91A SER* 1.3 57.9 + - - +
92A ASN* 2.8 27.2 + - - +
93A SER* 3.1 17.3 + - - -
95A PRO 3.0 28.1 + - - -
96A TYR* 3.3 13.9 - - - +
97A THR* 3.1 33.8 + - - +
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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