Contacts of the strand formed by residues 19 - 25 (chain D) in PDB entry 3W13
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 19 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 4.0 24.5 - - + -
13D VAL* 3.8 37.5 - - + -
18D LYS* 1.3 82.9 - - - +
20D THR* 1.3 69.4 + - - +
21D MET* 4.7 15.7 - - + -
79D LEU 3.5 1.0 - - - +
80D THR* 3.0 5.9 - - - +
81D ILE* 2.7 49.5 + - + +
84D VAL* 4.4 8.7 - - + -
109D LEU* 4.6 10.1 - - + -
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Residues in contact with THR 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 5.6 3.7 - - - +
18D LYS* 4.9 2.9 - - - +
19D VAL* 1.3 80.5 + - - +
21D MET* 1.3 60.7 + - - +
78D THR* 3.8 28.7 - - + +
79D LEU 3.1 9.6 - - - +
80D THR* 3.4 21.0 + - - +
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Residues in contact with MET 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D SER 3.8 6.3 - - - +
8D PRO* 4.3 9.9 - - + -
11D LEU* 6.1 3.4 - - + -
19D VAL* 4.7 11.7 - - + -
20D THR* 1.3 73.5 - - - +
22D SER* 1.3 62.3 + - - +
41D TRP* 4.3 13.5 - - + -
78D THR* 3.2 6.6 - - - -
79D LEU* 3.0 64.9 + - + +
81D ILE* 4.1 14.6 - - + -
92D TYR* 3.8 32.5 - - + -
107D THR* 3.3 39.5 - - + +
108D LYS 6.1 1.1 - - - +
109D LEU* 6.1 2.5 - - + -
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Residues in contact with SER 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D GLN* 3.3 13.3 + - - +
7D SER* 2.8 54.1 + - - +
21D MET* 1.3 74.7 - - - +
23D CYS* 1.3 64.4 + - - +
41D TRP* 4.4 2.2 - - - -
77D PHE 3.4 9.2 - - - -
78D THR* 4.2 9.4 - - - -
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Residues in contact with CYS 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D MET* 3.9 15.0 - - - -
5D SER 3.2 10.8 - - - -
6D GLN* 4.1 1.6 - - + +
22D SER* 1.3 77.1 - - - +
24D LYS* 1.3 74.8 + - - +
39D LEU* 4.6 5.8 - - - -
41D TRP* 3.8 12.6 - - + -
76D ASP* 3.8 3.5 - - - +
77D PHE* 2.9 35.7 + - + +
94D CYS* 2.1 52.5 - - + -
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Residues in contact with LYS 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D VAL 3.6 2.3 - - - +
4D MET* 3.1 12.8 - - - +
5D SER* 2.9 49.7 + - - +
23D CYS* 1.3 79.3 - - - +
25D SER* 1.3 77.7 + - - +
26D SER* 5.1 3.1 - - - +
75D THR* 3.3 15.5 - - - +
76D ASP* 3.5 20.9 - - - +
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Residues in contact with SER 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ILE* 3.8 6.2 - - - +
3D VAL 3.6 5.6 - - - -
4D MET* 3.7 24.7 - - - -
24D LYS* 1.3 86.4 - - - +
26D SER* 1.3 61.0 + - - +
27D GLN 2.9 27.1 + - - -
29D LEU* 3.7 21.1 - - - +
75D THR* 2.9 29.2 + - - +
77D PHE* 5.6 0.4 - - - -
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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