Contacts of the strand formed by residues 7 - 14 (chain X) in PDB entry 3NZA
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 LEU 7 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5X LYS 4.3 4.9 - - - +
6X SER* 1.3 82.8 - - - +
8X THR* 1.4 64.1 + - - +
56X LEU* 5.1 2.7 - - + -
98X LEU* 4.6 15.5 - - + -
102X LEU* 4.0 21.5 - - + -
120X ILE* 3.8 30.5 - - + +
122X VAL* 5.1 8.5 - - + -
132X ALA* 5.7 1.1 - - - -
135X HIS* 3.6 42.0 - - + +
137X LYS* 2.9 14.4 + - + -
138X LEU* 3.2 18.5 - - + +
139X ASP* 3.1 32.4 + - - +
140X ARG 3.8 0.3 + - - -
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Residues in contact with THR 8 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X SER* 5.2 1.4 + - - -
7X LEU* 1.4 76.8 + - - +
9X LEU* 1.3 71.5 + - - +
119X ARG* 5.7 1.4 - - - +
120X ILE 3.1 9.7 + - - -
121X PHE* 3.2 26.5 - - + -
122X VAL* 2.8 25.3 + - - +
138X LEU* 3.9 2.5 - - - -
139X ASP* 4.6 1.0 + - - -
140X ARG* 3.3 28.6 + - + +
142X MET* 3.7 22.7 - - + -
180X TRP* 3.6 18.2 - - + -
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Residues in contact with LEU 9 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X THR* 1.3 77.6 - - - +
10X ILE* 1.3 55.3 + - - +
11X VAL* 3.7 19.1 - - + -
122X VAL* 3.4 8.7 - - + +
129X TYR* 3.5 27.4 - - + +
132X ALA* 4.2 14.6 - - + -
133X MET* 3.7 22.9 - - + -
138X LEU* 3.6 9.8 - - + +
140X ARG 2.8 12.2 + - - +
141X ILE* 3.4 14.1 - - + -
142X MET 2.8 31.2 + - - -
156X PHE* 3.6 37.7 - - + -
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Residues in contact with ILE 10 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X LEU* 1.3 74.6 - - - +
11X VAL* 1.3 58.0 + - - +
35X TYR* 4.4 9.6 - - + -
36X PHE* 3.7 30.1 - - + -
39X VAL* 4.0 29.8 - - + -
40X THR* 3.9 10.3 - - + -
121X PHE* 4.2 9.6 - - + -
122X VAL 2.9 11.0 + - - +
123X ILE* 3.7 29.2 - - + -
129X TYR* 2.7 25.1 + - - -
142X MET* 3.5 25.1 - - + +
144X THR* 6.0 0.2 - - - +
207X D2K 3.0 25.4 + - - +
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Residues in contact with VAL 11 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X LEU* 3.7 17.9 - - + -
10X ILE* 1.3 77.5 - - - +
12X ALA* 1.3 64.6 + - - +
13X LEU* 4.3 13.0 - - + -
19X ILE* 3.9 14.4 - - + -
129X TYR* 3.3 33.0 - - + +
141X ILE* 4.1 10.5 - - + -
142X MET 3.1 11.3 + - - +
143X ALA* 4.2 4.0 - - - -
144X THR 2.8 29.8 + - - -
156X PHE* 3.9 10.5 - - + -
160X PHE* 5.0 0.4 - - + -
207X D2K 3.4 8.7 + - - -
208X NDP 3.4 8.3 - - - +
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Residues in contact with ALA 12 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X VAL* 1.3 73.4 - - - +
13X LEU* 1.3 64.2 + - - +
19X ILE* 3.7 2.6 - - - +
27X TRP* 3.7 19.8 - - + +
32X GLU* 4.1 11.7 - - - +
144X THR* 3.4 13.5 - - - +
146X ILE* 4.3 6.3 - - + -
207X D2K 3.5 18.4 + - + +
208X NDP 2.7 38.1 + - - +
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Residues in contact with LEU 13 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X VAL* 4.3 8.7 - - + -
12X ALA* 1.3 76.8 - - - +
14X THR* 1.3 69.0 + - - +
17X TYR* 3.6 33.2 - - + -
18X GLY 3.3 7.0 - - - +
19X ILE* 3.6 15.3 - - + -
27X TRP* 4.4 1.1 - - - -
143X ALA* 4.0 23.6 - - + -
144X THR 2.9 23.2 + - - +
145X ILE* 3.6 10.7 - - + -
146X ILE* 2.8 29.1 + - - +
156X PHE* 4.1 13.0 - - + -
160X PHE* 3.8 21.3 - - + -
161X ARG* 5.1 2.7 - - - -
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Residues in contact with THR 14 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X LEU* 1.3 80.2 - - - +
15X THR* 1.3 59.1 + - - +
16X SER* 3.1 14.4 + - - -
17X TYR* 2.8 19.2 + - - -
18X GLY* 3.0 38.6 + - - +
27X TRP* 3.8 21.8 - - + -
145X ILE* 3.7 8.1 - - - +
146X ILE* 3.3 8.7 - - + -
148X LYS 3.2 24.5 - - - +
149X ASP* 4.6 2.1 + - - -
150X ILE* 4.2 16.7 + - + +
152X CYS* 4.4 2.9 - - - -
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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