Contacts of the strand formed by residues 91 - 98 (chain A) in PDB entry 6NMY
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 CYS 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ILE* 5.2 1.6 - - - -
48A ALA* 4.1 4.7 - - + -
49A ASP 3.5 8.7 - - - +
50A THR* 4.6 0.2 - - - +
51A GLN* 3.6 9.3 + - - -
81A MET* 5.5 2.5 - - + -
86A CYS* 2.0 50.9 - - + -
88A HIS* 2.9 36.6 - - - +
89A PRO 3.7 1.8 - - - -
90A ARG* 1.3 77.3 - - - +
92A VAL* 1.3 60.5 + - - +
93A PRO* 3.7 9.3 - - + +
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Residues in contact with VAL 92 (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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48A ALA* 4.2 1.1 - - - -
49A ASP* 2.9 45.1 + - + +
50A THR 3.9 7.6 - - - +
51A GLN* 4.1 10.3 - - + +
54A GLN* 3.3 28.3 - - - +
77A LEU* 3.5 26.0 - - + -
91A CYS* 1.3 73.2 - - - +
93A PRO* 1.3 60.4 - - + +
94A ARG* 2.9 32.8 + - - +
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Residues in contact with PRO 93 (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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47A TRP 3.6 6.1 - - - +
48A ALA* 3.9 3.8 - - + -
77A LEU* 3.1 16.5 - - + +
78A SER* 3.0 40.8 + - - +
79A ASP 4.4 2.2 - - - -
80A ASP* 4.0 20.2 - - - +
81A MET* 3.5 31.2 - - + -
91A CYS* 3.7 9.2 - - + +
92A VAL* 1.3 90.0 - - + +
94A ARG* 1.3 62.3 + - - +
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Residues in contact with ARG 94 (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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46A ARG* 3.6 21.5 + - - +
47A TRP* 2.9 65.6 + - + +
49A ASP* 3.4 24.8 + - - +
54A GLN* 3.1 24.7 - - - +
58A ASN* 4.5 6.1 - - - +
59A VAL 4.6 3.6 + - - -
75A CYS* 4.4 8.2 - - + +
76A ASP 3.4 12.6 - - - +
77A LEU* 4.7 7.2 - - - +
78A SER* 3.5 9.5 + - - +
80A ASP 5.1 0.5 - - - +
92A VAL* 2.9 40.4 + - - +
93A PRO* 1.3 78.3 - - - +
95A ARG* 1.3 63.7 + - - +
96A CYS* 4.1 5.4 - - - -
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Residues in contact with ARG 95 (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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44A THR* 4.8 12.7 - - - +
45A CYS 3.5 6.5 - - - +
46A ARG* 3.4 41.9 - - + +
76A ASP* 2.9 35.8 + - + +
78A SER* 3.7 14.1 - - - -
94A ARG* 1.3 77.6 - - - +
96A CYS* 1.3 63.1 + - - +
97A VAL* 4.0 28.3 + - - +
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Residues in contact with CYS 96 (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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44A THR* 3.3 5.2 - - - -
45A CYS* 2.8 34.1 + - + +
47A TRP* 3.2 26.2 - - - -
61A LEU* 4.1 7.9 - - + -
73A VAL* 3.7 13.5 - - + -
74A SER 3.4 11.2 - - - +
75A CYS* 2.0 48.9 - - - +
94A ARG* 4.4 1.8 - - - -
95A ARG* 1.3 73.7 - - - +
97A VAL* 1.3 60.4 + - - +
98A ILE 4.1 0.9 - - - -
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Residues in contact with VAL 97 (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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42A HIS* 4.3 20.6 - - + +
43A ILE 3.5 5.8 - - - +
44A THR* 3.7 23.3 - - + -
73A VAL* 5.3 0.2 - - - -
74A SER* 4.2 10.1 + - - +
76A ASP* 6.0 2.2 - - - +
95A ARG* 4.4 25.4 - - - +
96A CYS* 1.3 77.0 - - - +
98A ILE* 1.3 59.5 + - - +
99A PRO* 4.0 5.6 - - + +
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Residues in contact with ILE 98 (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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42A HIS* 4.5 0.9 - - - -
43A ILE* 2.9 53.3 + - + +
45A CYS* 5.5 2.9 - - - -
63A ARG* 4.6 26.0 - - - +
71A GLU* 4.5 14.6 - - + +
72A PRO 5.0 3.6 - - - +
73A VAL* 4.1 39.7 - - + -
74A SER* 5.2 5.6 - - - +
96A CYS 4.1 0.4 - - - -
97A VAL* 1.3 73.4 - - - +
99A PRO* 1.3 73.6 - - + +
100A CYS* 5.3 0.4 - - + +
111A PHE* 5.1 7.6 - - + -
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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