Contacts of the strand formed by residues 25 - 29 (chain A) in PDB entry 2KBS
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 25 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.1 26.8 - - - +
24A GLY* 1.3 78.5 - - - +
26A SER* 1.3 74.5 + - - +
39A ILE* 3.8 20.0 - - + -
41A HIS 3.8 1.3 - - - -
42A VAL* 3.3 12.8 - - + -
48A SER* 2.9 27.1 - - - +
53A LEU* 4.2 3.4 - - + -
59A ILE* 5.6 1.6 - - - -
117B GLU* 5.8 0.2 - - - -
118B LEU* 2.9 39.5 + - - +
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Residues in contact with SER 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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25A CYS* 1.3 79.2 - - - +
27A ILE* 1.3 66.6 + - - +
39A ILE* 3.5 3.3 - - - +
40A SER* 2.7 42.3 + - - -
41A HIS* 3.2 15.5 + - - +
115B ILE* 4.1 4.7 - - - +
116B THR 2.8 19.8 + - - -
117B GLU* 3.2 26.9 + - - +
118B LEU* 4.2 0.4 - - - +
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Residues in contact with ILE 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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26A SER* 1.3 82.7 - - - +
28A SER* 1.3 59.4 + - - +
37A ILE* 3.8 14.8 - - + -
38A PHE 2.9 19.5 - - - +
39A ILE* 4.0 13.7 - - + -
40A SER* 4.0 2.0 - - - +
59A ILE* 4.2 5.4 - - + -
72A HIS* 3.5 14.2 - - + -
75A ALA* 4.2 12.1 - - + -
76A VAL* 3.2 37.7 - - + +
79A LEU* 5.8 0.4 - - + -
115B ILE* 3.1 4.5 - - - -
116B THR* 2.7 43.7 + - - -
118B LEU* 3.4 28.9 - - + -
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Residues in contact with SER 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 1.3 74.5 - - - +
29A SER* 1.3 65.8 + - - +
36A GLY 3.6 0.9 - - - +
37A ILE* 3.7 2.4 - - - +
38A PHE* 2.7 44.0 + - - -
40A SER* 4.0 8.7 + - - -
72A HIS* 4.1 5.3 - - - -
98A PHE* 5.2 11.2 - - - -
113B LEU* 3.4 19.8 + - - +
114B GLU 2.8 20.0 + - - -
115B ILE* 3.9 13.2 - - - +
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Residues in contact with SER 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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28A SER* 1.3 77.3 + - - +
30A GLY* 1.3 62.9 - - - +
36A GLY 3.6 10.1 + - - -
37A ILE* 5.0 0.9 - - - +
38A PHE* 3.8 2.2 - - - -
72A HIS* 3.2 39.7 + - - +
113B LEU* 2.9 34.7 - - - +
114B GLU* 3.3 10.6 + - - -
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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