Contacts of the strand formed by residues 39 - 43 (chain B) in PDB entry 3SSB
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 ILE 39 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B GLN* 3.3 2.9 - - - -
32B ASP* 2.8 43.1 + - + +
35B ARG* 3.7 22.7 - - + +
38B GLY* 1.3 78.4 - - - +
40B PHE* 1.3 63.9 + - - +
41B THR* 4.7 2.0 - - - +
74B HIS* 3.2 25.6 - - + +
77B ALA* 3.6 29.4 - - + +
78B GLY* 3.4 34.5 - - - +
81B TYR* 4.2 7.4 - - + -
100B ILE* 3.3 21.8 - - + +
102B SER* 5.6 1.1 - - - +
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Residues in contact with PHE 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ILE 4.8 3.6 - - - -
30B LEU 3.4 3.8 - - - -
31B GLN* 3.5 41.3 - - + -
33B ASN* 5.7 0.4 - - - -
37B ASN 3.3 27.1 - - - -
38B GLY* 3.6 15.9 - - - -
39B ILE* 1.3 74.8 - - - +
41B THR* 1.3 65.2 + - - +
42B TYR* 3.5 21.8 - - + +
54B LEU* 3.8 14.8 - - + -
99B ALA* 3.5 16.4 - - + -
100B ILE 2.8 14.8 + - - +
101B ARG* 3.3 24.8 - - + +
102B SER* 3.0 25.3 + - - +
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Residues in contact with THR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 3.0 25.2 + - + +
39B ILE* 4.7 1.6 - - - +
40B PHE* 1.3 75.8 + - - +
42B TYR* 1.3 68.7 + - - +
54B LEU* 3.6 5.4 - - - +
55B TRP* 2.9 27.1 + - + +
70B ALA* 3.8 30.5 - - + +
73B ALA* 4.3 12.3 - - + -
74B HIS* 2.8 35.1 + - - +
102B SER* 3.3 11.2 - - - +
104B VAL* 4.6 3.1 - - + -
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Residues in contact with TYR 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B PHE* 3.5 27.5 - - + +
41B THR* 1.3 77.3 - - - +
43B ASP* 1.3 60.0 + - - +
51B PRO* 3.2 43.1 - - + +
52B GLY 3.5 12.8 - - - -
53B SER 3.1 5.8 - - - +
54B LEU* 3.4 39.9 - - + +
55B TRP* 4.1 4.9 - - - +
101B ARG* 2.8 42.8 + - + -
102B SER 2.8 17.7 + - - -
103B SER* 3.3 4.9 - - - +
104B VAL* 3.0 31.0 + - - +
119B GLN* 5.3 0.2 - - - -
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Residues in contact with ASP 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A LYS* 5.0 4.8 + - - +
251A TYR* 3.9 2.8 + - - -
42B TYR* 1.3 73.1 - - - +
44B ALA* 1.3 60.5 + - - +
45B LYS* 2.8 47.5 + - + +
51B PRO 4.4 2.0 - - - -
52B GLY* 3.6 1.2 - - - -
53B SER* 2.8 34.5 + - - +
55B TRP* 3.5 29.4 - - + -
66B TYR* 2.8 34.8 + - - -
104B VAL 4.0 1.1 - - - -
105B HIS* 3.4 11.3 - - - -
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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