Contacts of the strand formed by residues 28 - 32 (chain C) in PDB entry 5IHB
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 SER 28 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B SER 4.8 0.4 + - - -
168B ALA 5.9 3.7 + - - -
169B CYS* 6.3 2.9 - - - -
170B GLU* 4.1 10.0 + - - +
193B HIS* 4.9 1.9 + - - -
26C GLN* 2.9 25.2 + - - +
27C GLU* 1.3 82.3 - - - +
29C VAL* 1.3 63.7 + - - +
30C THR* 4.7 4.3 + - - -
134C LEU* 4.3 0.7 - - - -
135C SER* 3.3 7.2 - - - -
137C HIS* 3.6 22.9 + - - -
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Residues in contact with VAL 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B GLU* 3.4 9.4 - - - +
26C GLN* 3.7 16.4 - - - +
28C SER* 1.3 77.1 + - - +
30C THR* 1.3 68.0 + - - +
31C VAL* 6.0 0.2 - - + -
37C VAL* 3.5 37.2 - - + -
39C VAL* 4.0 14.4 - - + -
105C ILE* 5.5 0.7 - - + -
134C LEU* 3.8 20.2 - - + -
135C SER 2.9 10.9 + - - +
136C VAL* 3.9 21.7 - - + +
137C HIS* 2.9 27.2 + - - +
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Residues in contact with THR 30 (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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38B LEU* 6.4 0.4 - - + -
93B LEU* 6.0 2.0 - - + -
170B GLU* 2.8 18.3 + - - +
171B GLN* 4.5 26.8 - - + +
28C SER* 4.7 5.0 + - - -
29C VAL* 1.3 81.0 + - - +
31C VAL* 1.3 64.8 + - - +
32C GLN* 6.2 0.2 - - + -
37C VAL* 4.7 4.3 - - - +
137C HIS* 3.3 16.4 - - + +
139C THR* 3.8 32.3 - - + +
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Residues in contact with VAL 31 (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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29C VAL* 5.9 0.9 - - + -
30C THR* 1.3 76.7 - - - +
32C GLN* 1.3 72.6 + - - +
35C LEU* 3.9 5.4 - - + +
36C CYS* 3.7 38.4 - - - +
37C VAL* 4.1 17.0 - - + -
105C ILE* 5.5 2.2 - - + -
108C ALA* 3.7 20.0 - - + -
136C VAL* 4.5 11.4 - - + -
137C HIS 3.0 12.4 + - - +
138C VAL* 3.1 13.6 - - + -
139C THR* 3.0 23.9 + - - -
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Residues in contact with GLN 32 (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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30C THR* 6.2 0.2 - - + -
31C VAL* 1.3 80.8 - - - +
33C GLU* 1.3 65.7 + - - +
34C GLY 3.3 0.3 + - - -
35C LEU* 2.9 34.5 + - + +
108C ALA* 4.0 1.7 - - - +
138C VAL* 4.3 0.9 - - - -
139C THR* 3.5 14.1 - - - +
140C ASP 3.6 16.5 + - - +
141C LEU* 3.3 8.3 - - - +
142C THR* 2.8 42.6 + - - +
143C HIS* 3.2 33.5 + - - -
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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