Contacts of the strand formed by residues 23 - 30 (chain A) in PDB entry 3OTC
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 TRP 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A CYS* 1.3 72.9 - - - +
24A VAL* 1.3 61.0 + - - +
25A VAL* 4.0 0.8 - - + +
69A VAL* 4.2 11.4 - - + -
81A VAL* 3.7 12.8 - - + -
82A PHE 3.4 20.0 - - - -
83A LYS* 4.1 6.3 - - + -
84A ARG* 3.7 40.8 - - + +
132A VAL 3.8 0.7 - - - +
133A VAL* 3.4 6.2 - - - +
134A TYR* 2.7 42.1 + - + +
135A PRO 4.8 2.5 - - - -
136A SER 3.5 21.9 + - - -
137A ASN* 2.7 30.2 + - - +
140A LEU* 3.6 33.2 - - + -
264A ILE* 3.5 26.7 - - + -
265A LEU* 3.9 24.7 - - + -
267A GLU* 6.0 1.8 - - + -
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Residues in contact with VAL 24 (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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18A CYS* 3.9 18.8 - - + -
22A CYS 3.6 1.3 + - - +
23A TRP* 1.3 74.7 - - - +
25A VAL* 1.3 64.9 + - - +
26A VAL* 4.8 0.7 - - + -
80A PHE 3.6 1.0 - - - +
81A VAL* 3.6 1.4 - - - -
82A PHE* 2.9 48.4 + - + +
86A THR* 5.2 2.7 - - + -
91A ARG* 3.6 26.9 - - - +
96A PHE* 3.8 38.6 - - + -
131A VAL* 4.0 20.9 - - + -
132A VAL 3.9 2.2 - - - -
133A VAL* 4.8 3.1 - - + +
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Residues in contact with VAL 25 (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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23A TRP 4.8 0.4 - - - +
24A VAL* 1.3 80.1 - - - +
26A VAL* 1.3 67.5 + - - +
27A ARG* 3.9 1.4 + - + +
79A SER* 4.2 14.1 - - - -
80A PHE 3.3 8.5 - - - +
81A VAL* 4.0 11.2 - - + -
130A ARG 3.7 0.2 - - - +
131A VAL* 3.4 4.2 - - - -
132A VAL* 2.9 40.2 + - + +
134A TYR* 3.8 22.4 - - + -
140A LEU* 3.8 29.4 - - + -
143A TYR* 3.9 29.2 - - + +
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Residues in contact with VAL 26 (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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24A VAL* 4.8 1.6 - - + -
25A VAL* 1.3 78.4 - - - +
27A ARG* 1.3 63.8 + - - +
28A LEU* 5.1 3.6 - - + -
79A SER* 3.4 1.6 - - - -
80A PHE* 2.9 36.3 + - + +
82A PHE* 3.8 24.0 - - + -
96A PHE* 3.8 26.5 - - + +
97A MET* 4.2 11.4 - - - +
100A VAL* 4.0 31.0 - - + -
129A GLY* 5.4 0.4 - - - -
130A ARG 3.2 14.6 - - - +
131A VAL* 3.9 9.4 - - + -
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Residues in contact with ARG 27 (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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25A VAL* 3.9 3.1 + - + -
26A VAL* 1.3 73.1 - - - +
28A LEU* 1.3 72.4 + - - +
29A ASP* 3.2 18.3 + - - +
77A GLU* 4.2 6.3 - - + -
78A TYR 3.7 3.8 - - - +
79A SER* 3.8 11.9 - - - +
128A ASP 3.7 0.7 - - - +
129A GLY* 3.3 5.2 - - - -
130A ARG* 3.1 79.1 + - + +
132A VAL* 5.4 3.8 - - + +
143A TYR* 3.0 39.6 + - - +
146A TRP* 3.9 21.9 - - - -
147A ARG* 3.7 26.0 - - - +
13B GLU* 4.0 11.3 + - - -
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A VAL* 5.1 2.9 - - + -
27A ARG* 1.3 75.3 - - - +
29A ASP* 1.3 62.4 + - - +
54A MET* 6.2 0.9 - - + -
77A GLU* 3.0 30.2 - - - +
78A TYR* 3.0 18.8 + - + +
80A PHE* 4.0 4.9 - - + -
100A VAL* 3.9 21.5 - - + +
101A ALA* 3.8 29.2 - - + +
104A PHE* 3.5 50.7 - - + -
127A PHE* 4.5 14.8 - - + -
128A ASP 3.2 13.2 - - - +
129A GLY* 4.0 8.7 - - - -
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Residues in contact with ASP 29 (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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27A ARG* 3.2 29.2 + - - +
28A LEU* 1.3 74.9 - - - +
30A GLY* 1.3 64.5 + - - +
76A ASP* 3.4 5.7 - - - +
77A GLU* 3.3 24.7 - - - +
127A PHE* 4.1 3.4 - - - -
128A ASP* 2.7 53.0 + - + +
130A ARG* 4.5 10.2 + - - +
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Residues in contact with GLY 30 (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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29A ASP* 1.3 74.6 - - - +
31A ARG* 1.3 64.6 + - - -
32A ASN 3.5 2.4 + - - -
33A PHE* 3.4 33.8 + - - +
76A ASP* 3.0 17.4 + - - +
127A PHE* 3.6 19.2 - - - -
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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