Contacts of the strand formed by residues 93 - 101 (chain A) in PDB entry 2NQY
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 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A TRP* 3.1 14.0 - - - -
88A THR* 3.0 47.2 + - + +
91A PRO* 3.8 17.0 - - + +
92A LEU* 1.3 79.9 - - - +
94A GLU* 1.3 74.4 + - - +
95A TYR* 4.1 7.7 + - + -
142A SER* 3.5 12.1 - - - +
144A TYR* 3.6 54.1 - - + +
172A ASN 4.0 0.9 - - - +
173A MET* 4.9 3.1 - - + -
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Residues in contact with GLU 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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85A TYR* 2.5 43.5 + - + +
86A GLY 3.5 3.4 - - - +
87A TRP* 3.4 26.0 - - + -
93A VAL* 1.3 73.2 - - - +
95A TYR* 1.3 62.0 + - - +
96A TYR* 4.1 5.8 - - + -
141A PHE* 3.7 8.4 - - + -
142A SER 3.0 6.6 + - - +
143A GLN* 2.7 61.1 + - + +
144A TYR 3.0 3.3 + - - -
1C XYP 2.7 35.7 + - - +
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Residues in contact with TYR 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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84A VAL* 4.5 11.9 - - + -
85A TYR* 3.5 21.1 - - - -
86A GLY* 2.9 61.2 + - - -
87A TRP* 3.5 15.9 - - - -
88A THR* 4.7 8.1 - - + -
93A VAL* 4.4 7.0 - - + -
94A GLU* 1.3 76.3 - - - +
96A TYR* 1.3 69.9 + - - +
97A ILE* 5.1 1.6 - - + -
144A TYR* 3.3 10.5 - - + +
163A PHE* 3.4 30.5 - + - -
166A TRP* 3.5 31.0 - + + -
173A MET* 5.1 2.2 - - - -
176A MET* 3.6 6.0 - - + +
178A GLU 2.8 21.9 + - - -
179A VAL* 3.3 18.9 - - - +
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Residues in contact with TYR 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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81A TYR* 4.0 10.4 - + - -
83A CYS* 3.9 20.2 - - - -
84A VAL 3.5 4.0 - - - -
85A TYR* 3.6 26.7 - + - -
94A GLU* 4.0 12.6 - - + -
95A TYR* 1.3 79.1 - - - +
97A ILE* 1.3 62.4 + - - +
98A VAL* 3.9 7.9 - - + -
143A GLN* 3.9 13.4 + - - -
144A TYR 2.8 7.7 + - - +
145A TRP* 3.4 58.5 - + + -
146A SER 2.9 24.4 + - - -
166A TRP* 3.3 9.5 - - - -
184A GLU* 2.8 35.8 + - - -
3001A XYP 5.1 1.7 - - - -
1C XYP 3.7 12.8 - - - -
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Residues in contact with ILE 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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83A CYS* 3.2 2.7 - - - -
84A VAL* 2.8 49.5 + - + +
95A TYR* 5.1 1.3 - - + -
96A TYR* 1.3 77.6 - - - +
98A VAL* 1.3 63.0 + - - +
99A ASP* 3.8 1.3 + - - +
122A TYR* 4.0 12.8 - - + -
146A SER* 3.4 4.9 - - - -
157A ILE* 4.0 23.7 - - + +
159A VAL* 4.0 28.5 - - + +
162A HIS* 3.6 52.0 - - + +
163A PHE* 4.8 1.8 - - + -
166A TRP* 4.0 18.2 - - + -
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Residues in contact with VAL 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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81A TYR* 4.2 12.6 - - + -
82A LEU 3.9 2.5 - - - +
83A CYS* 3.8 10.8 - - + -
96A TYR* 3.9 23.8 - - + -
97A ILE* 1.3 74.3 - - - +
99A ASP* 1.3 62.2 + - - +
100A SER 3.1 29.4 - - - +
101A TRP* 4.3 10.3 - - + -
106A PRO* 4.4 11.4 - - + -
122A TYR* 3.7 2.5 - - - -
145A TRP* 4.1 18.4 - - + -
146A SER 2.8 15.7 + - - +
147A THR* 4.3 8.7 - - + +
148A ARG* 3.0 28.6 + - - +
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Residues in contact with ASP 99 (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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70A TYR* 2.4 37.1 + - + +
82A LEU* 3.0 10.3 + - + +
97A ILE* 3.8 2.3 + - - +
98A VAL* 1.3 73.0 - - - +
100A SER* 1.3 59.7 + - - +
101A TRP* 3.9 6.2 - - - -
122A TYR* 2.6 35.4 + - - -
148A ARG* 3.7 5.9 - - - +
150A SER 4.0 3.5 - - - +
151A LYS* 3.3 7.4 - - - -
152A ARG* 2.8 53.2 + - - +
157A ILE* 3.6 14.5 - - + +
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Residues in contact with SER 100 (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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74A PHE* 3.8 23.1 - - - -
81A TYR* 3.5 0.5 - - - -
82A LEU* 2.9 32.6 + - - -
98A VAL* 3.1 13.0 - - - +
99A ASP* 1.3 78.7 - - - +
101A TRP* 1.3 74.6 + - - +
151A LYS* 3.5 21.6 - - - +
152A ARG 3.5 14.6 - - - -
153A THR* 4.1 7.8 - - - +
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Residues in contact with TRP 101 (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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74A PHE* 3.8 14.1 - - - -
76A PRO* 4.6 1.2 - - - +
80A ALA 3.0 14.8 - - - +
81A TYR* 4.3 2.5 - - + -
98A VAL* 4.3 8.7 - - + -
99A ASP 3.9 16.6 - - - -
100A SER* 1.3 87.8 + - - +
102A GLY* 1.3 72.2 + - - +
103A ASN 5.4 0.4 - - - -
104A TRP 3.5 29.2 - - - +
105A ARG* 3.6 32.4 - - + +
106A PRO* 4.1 8.5 - - + -
147A THR* 4.2 9.9 - - + -
148A ARG 3.2 30.1 - - - -
149A ARG 4.2 5.8 - - - -
150A SER* 4.1 1.8 - - - -
151A LYS* 3.1 56.9 + - + +
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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