Contacts of the strand formed by residues 116 - 122 (chain X) in PDB entry 3NZ9
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 GLN 116 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50X GLU* 3.4 31.4 + - + +
51X SER* 3.4 15.2 - - - +
52X MET* 2.9 27.2 + - - +
109X TYR* 4.7 5.5 - - - +
110X GLY 2.5 32.6 + - - +
111X SER* 3.5 15.0 + - - -
113X SER 3.1 16.0 + - - -
115X VAL* 1.3 79.8 + - - +
117X ILE* 1.3 65.0 + - - +
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Residues in contact with ILE 117 (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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5X LYS* 3.2 32.2 + - + -
51X SER* 5.0 2.4 + - - -
52X MET 3.4 4.7 - - - +
54X VAL* 4.0 19.5 - - + -
76X ILE* 4.4 3.8 - - + -
105X LEU* 3.8 32.1 - - + +
106X TYR* 4.4 15.0 - - + -
109X TYR* 3.8 35.2 + - + +
116X GLN* 1.3 78.2 + - - +
118X ASN* 1.4 64.4 + - - +
119X ARG 4.3 0.7 - - - +
120X ILE* 3.7 28.9 - - + -
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Residues in contact with ASN 118 (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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5X LYS* 2.9 32.1 + - - +
42X PHE 3.7 11.8 - - - +
43X VAL* 3.8 20.3 - - + +
44X PRO* 4.0 10.8 - - - +
47X ASP* 4.9 10.5 + - - +
51X SER* 4.0 17.0 + - - -
52X MET 2.8 13.5 + - - +
53X ASN* 3.0 19.9 - - - +
116X GLN 3.8 0.8 + - - -
117X ILE* 1.4 71.5 - - - +
119X ARG* 1.3 76.6 + - - +
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Residues in contact with ARG 119 (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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5X LYS* 5.3 0.2 - - - -
6X SER 5.9 0.2 - - - -
8X THR* 5.9 1.3 - - - +
39X VAL* 5.4 2.0 + - - +
42X PHE* 3.9 25.9 + - - +
44X PRO* 5.2 7.8 - - - +
53X ASN* 2.9 13.6 + - - +
54X VAL* 2.9 24.3 + - - +
117X ILE* 4.4 0.9 - - - +
118X ASN* 1.3 99.7 + - - +
120X ILE* 1.3 65.3 + - - +
121X PHE* 3.8 17.6 - - + -
180X TRP* 2.9 87.0 + - + +
181X VAL* 4.5 1.2 - - - +
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Residues in contact with ILE 120 (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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5X LYS* 4.1 15.2 - - + +
6X SER 4.3 7.1 + - - +
7X LEU* 3.7 20.0 - - + -
8X THR* 3.1 27.0 + - - -
54X VAL* 3.7 13.9 - - + -
56X LEU* 3.7 32.3 - - + -
102X LEU* 3.7 22.9 - - + -
105X LEU* 4.8 6.1 - - + -
106X TYR* 3.9 20.0 - - + +
117X ILE* 3.7 23.6 - - + -
119X ARG* 1.3 78.5 - - - +
121X PHE* 1.3 63.5 + - - +
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Residues in contact with PHE 121 (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* 3.1 38.4 - - + -
10X ILE* 4.3 10.3 - - + -
39X VAL* 3.5 39.0 - - + -
40X THR* 3.9 27.1 - - + -
53X ASN* 4.1 9.0 - - + -
54X VAL 2.9 17.4 + - - +
55X VAL* 3.5 0.8 - - + -
56X LEU* 2.8 36.0 + - - +
119X ARG* 3.8 25.4 - - + -
120X ILE* 1.3 74.2 - - - +
122X VAL* 1.3 57.0 + - - +
123X ILE* 4.1 15.9 - - + -
142X MET* 4.7 0.9 - - + -
180X TRP* 3.7 23.6 - + - -
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Residues in contact with VAL 122 (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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7X LEU* 4.9 14.6 - - + -
8X THR 2.9 11.9 + - - +
9X LEU* 3.5 5.1 - - + -
10X ILE* 3.0 26.2 + - - +
56X LEU* 3.4 13.2 - - + -
98X LEU* 4.0 24.9 - - + -
121X PHE* 1.3 74.1 - - - +
123X ILE* 1.3 62.4 + - - +
124X GLY 4.0 1.3 - - - +
128X LEU* 3.7 24.7 - - + +
129X TYR* 3.8 23.2 - - + -
132X ALA* 4.1 25.4 - - + -
138X LEU* 5.7 0.2 - - + -
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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