Contacts of the strand formed by residues 12 - 18 (chain A) in PDB entry 5V35
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 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ASN 4.7 8.8 + - - -
9A VAL* 3.5 31.9 + - + +
10A GLU 3.2 10.6 - - - +
11A GLY* 1.3 89.5 - - - +
13A LYS* 1.3 65.0 + - - +
14A LYS* 4.0 4.5 + - + +
71A PHE* 3.9 29.8 - - + -
74A ILE* 6.1 0.4 - - + -
75A LEU* 4.3 21.5 - - + -
87A PHE* 4.9 6.5 - - + -
88A TRP* 3.4 14.5 - - - +
89A CYS* 4.8 3.4 - - - -
93A HIS* 4.1 2.2 - - + +
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Residues in contact with LYS 13 (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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12A VAL* 1.3 73.2 - - - +
14A LYS* 1.3 62.1 + - - +
15A THR* 5.0 5.5 - - + +
86A GLU 3.8 0.7 - - - +
87A PHE* 3.5 1.2 - - - -
88A TRP* 2.7 61.2 + - + +
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Residues in contact with LYS 14 (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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8A ASN* 5.0 12.8 - - - +
12A VAL* 4.0 5.8 + - + -
13A LYS* 1.3 71.9 - - - +
15A THR* 1.3 76.2 + - - +
16A ILE* 3.9 15.1 - - + +
78A SER* 2.7 36.6 + - - +
79A MET* 3.9 3.2 - - - +
83A GLU* 2.7 30.6 + - - -
85A ALA* 3.7 15.5 - - + -
86A GLU 3.5 6.3 - - - +
87A PHE* 3.6 27.6 - - + +
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Residues in contact with THR 15 (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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13A LYS* 5.0 6.7 - - + +
14A LYS* 1.3 84.8 - - - +
16A ILE* 1.3 65.8 + - - +
17A LEU* 4.1 5.9 - - - +
86A GLU* 2.9 53.1 + - - +
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Residues in contact with ILE 16 (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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14A LYS* 3.9 15.3 - - + +
15A THR* 1.3 74.3 - - - +
17A LEU* 1.3 66.5 + - - +
18A HIS 3.8 2.5 - - - +
19A GLY* 3.6 31.9 - - - +
83A GLU* 3.5 33.0 - - + +
84A VAL 4.0 6.1 - - - +
85A ALA* 4.4 1.6 - - - +
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Residues in contact with LEU 17 (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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15A THR* 4.1 17.9 - - - +
16A ILE* 1.3 81.8 - - - +
18A HIS* 1.3 64.7 + - + +
19A GLY 4.2 0.4 - - - -
84A VAL* 2.8 34.0 + - + +
86A GLU* 4.4 24.9 - - + +
150A VAL* 4.6 11.2 - - + -
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Residues in contact with HIS 18 (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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16A ILE* 4.0 3.1 - - - -
17A LEU* 1.3 79.6 - - + +
19A GLY* 1.3 73.7 + - - +
20A GLY* 5.2 0.2 - - - -
82A HIS* 3.3 24.4 + - + +
83A GLU* 3.3 1.9 - - - -
84A VAL* 3.0 44.2 + - + -
152A GLU* 5.7 1.8 - - - -
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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