Contacts of the strand formed by residues 5 - 14 (chain B) in PDB entry 5IZL
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 ARG 5 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B ALA* 4.2 11.1 - - - +
3B GLY 4.3 6.4 + - - -
4B ARG* 1.3 81.3 - - - +
6B VAL* 1.3 63.9 + - - +
57B SER* 3.8 25.5 + - - -
68B LEU* 3.8 6.3 - - - +
85B LEU* 3.3 41.2 - - + +
87B GLN* 3.8 19.8 + - + +
273B PHE* 2.6 86.8 + - + +
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Residues in contact with VAL 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ARG* 1.3 74.3 - - - +
7B ASN* 1.3 62.7 + - - +
8B VAL* 5.3 0.2 - - + -
60B LEU* 4.1 23.8 - - + -
64B LEU* 4.6 5.2 - - + +
67B SER* 3.5 28.0 - - - +
68B LEU* 3.6 19.3 - - + -
85B LEU 3.3 3.4 + - - -
86B LEU* 3.5 11.9 - - + +
87B GLN* 2.6 35.5 + - - +
215B ILE* 4.0 24.2 - - + -
218B ARG* 5.7 1.8 - - - +
284B ASP* 5.8 2.5 - - - +
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Residues in contact with ASN 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ARG 4.0 1.0 + - - -
6B VAL* 1.3 80.7 - - - +
8B VAL* 1.3 66.1 + - - +
9B ASN* 3.2 17.6 + - - -
87B GLN* 2.9 23.8 + - - +
89B THR* 2.4 29.7 + - - -
218B ARG* 3.2 18.0 + - - -
272B MET* 5.6 0.2 - - - -
273B PHE* 4.2 11.4 - - + -
283B GLY 2.9 29.9 + - - +
284B ASP* 4.7 13.6 + - - +
285B ARG* 3.9 16.4 - - - +
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Residues in contact with VAL 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL 5.2 0.2 - - - -
7B ASN* 1.3 81.2 - - - +
9B ASN* 1.3 67.3 + - - +
10B VAL* 3.9 13.1 + - + -
86B LEU* 3.7 23.8 - - + -
87B GLN 2.8 11.1 + - - +
88B VAL* 3.4 6.8 - - + +
89B THR 2.6 32.2 + - - -
111B ASP* 3.8 16.2 - - + +
213B ILE* 3.8 31.6 - - + -
215B ILE* 4.2 19.7 - - + -
218B ARG* 4.0 6.1 - - - +
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Residues in contact with ASN 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ASN* 3.2 16.3 + - - +
8B VAL* 1.3 73.5 - - - +
10B VAL* 1.3 62.3 + - - +
53B PHE* 5.2 0.4 - - - -
89B THR* 3.2 28.3 - - - +
91B VAL* 4.2 10.6 - - + +
109B ILE* 3.1 28.8 + - - +
110B ILE* 4.1 2.7 - - - -
111B ASP* 3.0 36.2 + - - +
112B LEU 3.9 0.2 + - - -
218B ARG* 4.8 0.8 - - - +
244B THR* 3.2 37.2 + - - +
283B GLY 4.9 1.1 + - - -
285B ARG* 4.5 5.4 - - - +
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Residues in contact with VAL 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 4.0 7.4 - - + -
9B ASN* 1.3 78.1 - - - +
11B GLY* 1.3 58.0 + - - +
88B VAL* 4.1 20.2 - - + -
89B THR 2.8 8.4 + - - +
90B LEU* 3.2 10.5 - - + +
91B VAL* 2.7 29.2 + - - +
110B ILE* 4.3 1.8 - - - -
112B LEU* 3.6 28.3 - - + +
114B MET* 3.7 27.6 - - + -
209B LEU* 4.4 5.4 - - + -
213B ILE* 3.8 29.2 - - + -
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Residues in contact with GLY 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 1.3 73.8 - - - +
12B VAL* 1.3 64.3 + - - +
13B LEU* 3.8 7.0 - - - -
91B VAL* 3.2 10.3 - - - -
93B CYS* 5.4 0.4 - - - -
110B ILE* 3.9 23.4 - - - +
112B LEU 3.2 11.3 + - - -
113B MET* 4.8 0.2 - - - -
114B MET* 3.0 31.2 + - - +
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Residues in contact with VAL 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLY* 1.3 76.7 - - - +
13B LEU* 1.3 57.8 + - - +
20B LYS* 3.6 38.8 - - + +
23B LEU* 4.2 9.2 - - + -
24B ALA* 4.4 14.1 - - + -
90B LEU* 4.3 14.4 - - + -
91B VAL 2.8 14.8 + - - +
92B ASP* 4.0 14.1 - - - +
93B CYS* 3.1 23.4 + - - +
114B MET* 3.9 17.5 - - + +
116B VAL* 3.6 20.9 - - + -
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLY* 3.8 17.7 - - - -
12B VAL* 1.3 80.0 - - - +
14B GLY* 1.3 59.4 + - - +
20B LYS* 3.6 5.6 - - - -
93B CYS* 3.9 23.3 - - + -
94B PRO 5.5 0.2 - - - -
103B ILE* 3.8 24.5 - - + -
107B ALA* 4.8 13.9 - - + -
110B ILE* 4.3 7.2 - - + -
113B MET* 3.8 42.4 - - + -
114B MET 3.0 11.5 + - - +
115B LEU* 4.3 1.8 - - - -
116B VAL* 2.9 30.7 + - - +
130B CYS* 4.1 15.0 - - + +
133B ILE* 5.4 2.0 - - + -
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Residues in contact with GLY 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 1.3 78.9 - - - +
15B HIS* 1.3 70.1 + - - +
18B SER* 4.1 0.7 - - - -
20B LYS* 3.4 14.3 + - - +
94B PRO 4.3 2.2 + - - +
95B GLY* 3.7 10.9 - - - +
103B ILE* 5.4 0.5 - - - +
115B LEU* 4.1 11.0 - - - -
116B VAL 3.8 13.5 - - - -
126B GLN* 4.5 7.5 - - - +
130B CYS* 4.0 11.0 - - - -
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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