Contacts of the strand formed by residues 84 - 89 (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 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ILE 3.9 0.2 - - - -
17A LEU* 2.8 52.1 + - + -
18A HIS* 3.0 30.4 + - + +
82A HIS 4.3 4.5 - - - +
83A GLU* 1.3 79.5 - - - +
85A ALA* 1.3 57.7 + - - +
150A VAL* 4.1 13.9 - - + -
151A ILE 3.2 10.5 - - - +
152A GLU* 4.0 28.5 - - + +
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Residues in contact with ALA 85 (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* 3.7 30.5 - - - -
15A THR 3.7 7.2 - - - +
16A ILE* 4.6 1.6 - - - -
17A LEU* 4.3 4.7 - - - +
79A MET* 3.7 11.2 - - + -
83A GLU* 3.8 4.0 - - - +
84A VAL* 1.3 75.3 - - - +
86A GLU* 1.3 61.3 + - - +
87A PHE* 3.7 18.0 - - + -
149A PHE 4.0 0.5 - - - +
150A VAL* 3.4 2.4 - - - +
151A ILE* 2.8 31.2 + - - -
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Residues in contact with GLU 86 (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 3.8 1.0 - - - +
14A LYS* 3.5 3.1 - - - +
15A THR* 2.9 53.3 + - - +
17A LEU* 4.4 17.1 - - + +
46A ARG* 2.9 41.3 + - - -
85A ALA* 1.3 73.4 - - - +
87A PHE* 1.3 60.9 + - - +
88A TRP* 4.1 3.0 + - - +
148A VAL* 3.2 23.2 - - + +
149A PHE 3.5 2.7 - - - -
150A VAL* 3.8 17.0 - - + +
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Residues in contact with PHE 87 (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* 4.9 4.5 - - + -
13A LYS 3.5 4.0 - - - -
14A LYS* 3.6 36.3 - - + -
75A LEU* 3.1 64.4 - - + -
78A SER* 3.7 7.4 - - - -
79A MET* 3.7 26.5 - - + -
85A ALA* 3.7 13.7 - - + -
86A GLU* 1.3 73.0 - - - +
88A TRP* 1.3 62.8 + - - +
89A CYS* 3.7 7.1 - - - -
147A LEU 3.6 1.9 - - - +
148A VAL* 3.5 4.4 - - - -
149A PHE* 2.8 35.9 + - + +
151A ILE* 3.7 27.6 - - + -
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Residues in contact with TRP 88 (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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11A GLY* 4.1 11.0 - - - -
12A VAL* 3.4 6.1 - - - +
13A LYS* 2.7 59.6 + - + +
42A CYS* 3.4 34.6 - - - +
86A GLU* 4.1 4.1 - - - +
87A PHE* 1.3 73.3 - - - +
89A CYS* 1.3 64.7 + - - +
90A ASP* 3.6 38.6 - - + -
146A PRO* 3.8 26.8 - - + +
147A LEU 3.8 1.8 - - - -
148A VAL* 4.2 13.4 - - + +
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Residues in contact with CYS 89 (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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11A GLY 3.8 3.8 - - - -
12A VAL* 4.8 4.7 - - - -
71A PHE* 3.8 33.0 - - + -
75A LEU* 4.2 8.3 - - - -
87A PHE* 3.7 14.8 - - - -
88A TRP* 1.3 85.2 - - - +
90A ASP* 1.3 62.8 + - - +
93A HIS* 5.0 0.9 - - + -
94A THR* 3.7 9.4 - - + +
146A PRO* 2.9 30.2 - - - +
147A LEU 2.9 16.9 + - - +
149A PHE* 3.8 22.2 - - + -
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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