Contacts of the strand formed by residues 94 - 103 (chain Q) in PDB entry 2NX5
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 ILE 94 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10Q THR* 4.1 10.5 - - + -
11Q ALA 3.5 1.8 - - - -
12Q MET* 4.4 26.0 - - + -
13Q SER 5.4 0.9 - - - +
92Q SER* 4.3 15.0 - - - +
93Q HIS* 1.3 81.3 - - - +
95Q ILE* 1.3 64.7 + - - +
96Q GLN* 3.6 34.5 - - + +
117Q ALA 3.8 0.5 - - - +
118Q TYR* 3.4 6.1 - - - -
119Q ASP* 2.9 35.9 + - - +
31R HIS* 4.4 9.2 - - + -
32R PRO* 4.1 26.5 - - + -
33R SER* 4.9 6.5 - - - +
62R PHE* 4.1 8.3 - - + -
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Residues in contact with ILE 95 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Q TYR* 4.4 0.9 - - + +
10Q THR* 3.3 4.2 - - - -
11Q ALA* 2.8 43.3 + - + +
74Q TYR* 3.7 33.2 - - + +
77Q SER* 5.4 1.1 - - - -
78Q LEU* 3.3 37.9 - - + +
81Q LEU* 3.5 27.1 - - + -
94Q ILE* 1.3 73.0 - - - +
96Q GLN* 1.3 69.3 + - - +
116Q SER* 6.0 0.2 - - - -
117Q ALA 3.5 5.6 - - - +
118Q TYR* 3.6 27.1 - - + -
11S TYR* 4.9 12.8 - - + -
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Residues in contact with GLN 96 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Q TYR* 3.4 3.8 - - - -
10Q THR* 4.0 12.1 - - - +
94Q ILE* 3.6 17.5 - - + +
95Q ILE* 1.3 78.5 - - - +
97Q ARG* 1.3 62.3 + - - +
116Q SER* 3.3 5.9 + - - -
117Q ALA* 2.9 33.7 + - - +
120Q GLY 4.0 6.1 + - - -
31R HIS* 2.6 31.6 + - - -
56R PHE* 3.3 27.2 - - + -
60R TRP* 2.7 50.4 + - + +
62R PHE* 3.8 7.5 - - - -
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Residues in contact with ARG 97 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q TYR 3.7 1.2 - - - +
8Q PHE* 3.4 5.0 - - - -
9Q TYR* 2.8 50.2 + - + +
74Q TYR* 3.2 27.3 + - + +
96Q GLN* 1.3 76.2 - - - +
98Q MET* 1.3 69.7 + - - +
99Q TYR* 4.1 17.5 - - + -
114Q ASP* 2.7 30.2 + - - +
115Q GLN 3.4 7.4 - - - +
116Q SER* 3.4 13.7 - - - +
147Q TRP* 4.8 10.3 - - - -
152Q VAL* 5.8 0.4 - - - +
156Q LEU* 3.3 31.9 - - - +
56R PHE* 3.8 2.4 - - - -
60R TRP* 4.4 0.7 - - - -
3S LEU* 4.5 4.4 - - - +
5S GLN* 3.3 21.4 + - - +
9S THR* 5.1 6.5 + - - +
11S TYR* 3.4 21.1 + - - +
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Residues in contact with MET 98 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Q ARG* 5.7 4.7 - - - +
7Q TYR 3.6 5.6 - - - +
8Q PHE* 3.8 26.0 - - + +
97Q ARG* 1.3 72.1 - - - +
99Q TYR* 1.3 61.7 + - - +
113Q HIS* 4.3 1.5 - - - +
114Q ASP* 3.3 2.8 + - - +
115Q GLN* 2.8 74.4 + - + +
56R PHE* 3.5 30.3 - - + -
57R SER 4.2 0.2 - - - +
58R LYS* 4.1 38.8 - - + +
60R TRP* 3.8 11.0 - - + -
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Residues in contact with TYR 99 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Q ARG* 3.6 7.8 - - - +
7Q TYR* 2.7 70.0 + + + -
9Q TYR* 2.9 39.8 + + - -
97Q ARG* 4.1 21.5 - - + -
98Q MET* 1.3 76.0 - - - +
100Q GLY* 1.3 59.3 + - - +
113Q HIS 3.1 13.0 - - - +
114Q ASP* 4.1 13.2 - - + +
156Q LEU* 5.0 5.4 - - + -
159Q TYR* 3.6 32.5 - + - -
160Q LEU* 4.9 2.2 - - + -
2S PRO* 3.3 9.9 - - - +
3S LEU* 2.8 34.2 + - + -
5S GLN* 4.7 1.6 - - - -
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Residues in contact with GLY 100 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Q MET 3.1 14.4 - - - -
6Q ARG* 3.5 16.0 - - - +
7Q TYR* 6.2 0.4 - - - -
99Q TYR* 1.3 79.0 - - - +
101Q CYS* 1.3 60.7 + - - -
112Q GLY* 3.9 0.2 - - - -
113Q HIS* 3.0 32.4 + - - -
160Q LEU* 3.5 12.3 - - - +
164Q CYS* 4.6 3.4 - - - -
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Residues in contact with CYS 101 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Q SER* 3.3 6.1 - - - -
5Q MET* 3.1 31.1 + - - -
6Q ARG* 4.2 0.6 - - - +
100Q GLY* 1.3 73.6 - - - -
102Q ASP* 1.3 63.9 - - - +
103Q LEU* 5.9 0.4 - - - -
109Q LEU* 4.0 11.2 - - + -
111Q ARG 4.0 3.6 - - - -
112Q GLY* 4.8 0.2 - - - -
160Q LEU* 4.0 16.6 - - + +
164Q CYS* 2.0 60.8 - - + -
165Q VAL* 4.0 4.7 - - - -
168Q LEU* 4.0 13.9 - - - +
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Residues in contact with ASP 102 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Q SER* 3.4 18.6 - - - -
6Q ARG* 2.7 20.7 + - - -
101Q CYS* 1.3 72.7 - - - +
103Q LEU* 1.3 58.8 + - - +
109Q LEU* 3.3 11.1 - - - +
110Q LEU* 2.7 47.1 + - + +
111Q ARG* 3.2 15.0 + - - +
113Q HIS* 2.6 29.9 + - - -
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Residues in contact with LEU 103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Q SER* 3.3 6.6 - - - -
3Q HIS* 2.7 43.7 + - + +
101Q CYS* 5.8 0.4 - - - -
102Q ASP* 1.3 74.9 - - - +
104Q GLY* 1.3 63.2 + - - +
107Q GLY* 3.2 29.2 - - - +
108Q ARG 3.4 0.9 - - - +
109Q LEU* 3.6 23.3 - - + +
110Q LEU* 4.4 3.1 - - - +
165Q VAL* 4.1 22.0 - - + -
168Q LEU* 3.7 26.9 - - + -
169Q ARG* 3.9 28.5 - - + +
172Q LEU* 4.4 9.9 - - + -
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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