Contacts of the strand formed by residues 22 - 30 (chain C) in PDB entry 3B4V
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 CYS 22 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C TRP* 3.7 28.6 - - + -
14C LEU 4.1 4.5 - - - -
15C GLN* 3.7 24.5 - - - -
20C ALA 4.8 0.7 - - - -
21C THR* 1.3 77.4 - - - +
23C SER* 1.3 58.7 + - - +
44C ALA* 3.9 0.4 - - - -
59C GLY* 4.0 5.4 - - - +
62C GLY* 5.4 0.5 - - - -
64C VAL* 3.5 27.9 + - + +
66C CYS* 2.0 52.6 - - + +
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Residues in contact with SER 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B SER* 4.3 3.1 + - - -
13C TRP* 3.5 13.8 - - - -
14C LEU 3.9 1.0 + - - -
16C GLN* 3.4 27.5 + - - +
21C THR* 3.6 8.8 + - - -
22C CYS* 1.3 74.5 - - - +
24C LEU* 1.3 66.9 + - - +
25C VAL* 3.7 3.1 + - - +
56C ASN* 5.1 0.5 - - - +
59C GLY* 4.1 21.3 - - - -
60C PHE* 4.9 12.9 - - - -
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Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B GLY* 4.5 21.5 - - - +
2B LEU* 4.8 10.5 - - + -
55B SER* 3.4 31.2 - - - +
56B LEU 5.9 0.4 - - - +
13C TRP* 3.5 4.6 - - - -
14C LEU* 2.8 67.0 + - + +
16C GLN* 3.4 25.6 - - - +
23C SER* 1.3 79.7 + - - +
25C VAL* 1.3 63.7 + - - +
26C LEU* 3.5 3.9 + - + -
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Residues in contact with VAL 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B THR 5.4 1.3 - - - +
53B GLY 4.7 3.3 - - - +
54B SER 4.8 0.3 - - - -
55B SER* 3.2 31.4 + - - +
11C VAL* 4.3 15.5 - - + -
12C CYS 4.0 3.1 - - - -
13C TRP* 3.5 33.2 - - + -
23C SER 3.7 1.9 + - - +
24C LEU* 1.3 69.6 - - - +
26C LEU* 1.3 64.7 + - - +
27C GLN* 4.0 15.7 - - - +
28C THR* 4.4 11.4 - - + -
55C ILE* 4.7 5.6 - - + +
56C ASN* 4.6 28.3 - - - +
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Residues in contact with LEU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LEU* 4.2 31.4 - - + -
51B THR 3.3 11.1 - - - +
53B GLY 4.1 14.8 + - - +
12C CYS* 2.8 18.6 + - - +
13C TRP 3.4 26.5 - - - +
14C LEU* 3.9 23.6 - - + -
24C LEU* 3.5 4.2 + - + +
25C VAL* 1.3 78.4 - - - +
27C GLN* 1.3 70.8 + - + +
40C ASN* 6.2 1.3 - - - +
43C THR* 3.9 13.9 - - - +
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Residues in contact with GLN 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B THR* 3.3 20.6 - - - +
11C VAL* 3.4 5.5 - - - +
12C CYS* 2.7 39.4 + - + -
25C VAL* 4.3 2.7 - - - -
26C LEU* 1.3 90.4 - - + +
28C THR* 1.3 62.1 + - - +
30C VAL* 3.4 36.4 - - + +
34C GLU* 4.1 13.6 + - - +
35C CYS* 5.2 3.6 - - - -
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Residues in contact with THR 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLY 4.6 2.1 + - - -
51B THR* 2.6 43.5 + - - -
10C GLY 4.2 2.7 - - - -
11C VAL* 4.0 17.0 - - + -
25C VAL* 4.4 11.9 - - + +
27C GLN* 1.3 76.5 - - - +
29C ASP* 1.3 73.0 + - - +
30C VAL* 3.3 8.0 + - - +
49C THR* 6.4 0.9 - - + -
55C ILE* 4.2 22.7 - - + -
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Residues in contact with ASP 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B THR* 4.4 5.3 + - - +
9C GLY* 4.0 23.7 + - - +
10C GLY 3.1 10.1 + - - -
11C VAL* 4.6 1.6 - - - +
28C THR* 1.3 78.9 - - - +
30C VAL* 1.3 62.2 + - - +
34C GLU* 5.0 0.5 - - - +
49C THR* 6.3 0.6 - - - +
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Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B THR* 5.4 1.6 - - + +
9C GLY* 3.9 3.3 - - - -
10C GLY 2.8 33.4 + - - +
12C CYS* 3.8 16.4 - - + +
27C GLN* 3.4 55.4 - - + +
28C THR 3.8 5.6 - - - +
29C ASP* 1.3 78.4 - - - +
31C THR* 1.3 61.0 + - - +
34C GLU* 3.7 25.8 - - + +
35C CYS* 4.4 3.8 - - + +
45C TRP* 2.8 18.8 + - - +
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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