Contacts of the strand formed by residues 108 - 112 (chain C) in PDB entry 3SRH
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 ALA 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69C ASN 2.9 7.8 + - - +
70C VAL* 3.8 26.7 - - + -
71C ALA* 2.8 27.4 + - - +
106C PRO 4.2 0.6 - - - -
107C VAL* 1.3 77.9 - - - +
109C VAL* 1.3 59.8 + - - +
237C ASP* 3.4 14.6 - - + +
238C MET* 3.8 15.5 - - + -
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Residues in contact with VAL 109 (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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70C VAL* 4.5 0.7 - - - -
71C ALA* 3.9 7.9 - - + +
73C LEU* 3.9 22.9 - - + -
87C ILE* 4.0 22.0 - - + -
90C VAL* 4.8 10.8 - - + -
91C ARG* 4.4 28.9 - - + +
107C VAL 4.5 6.1 - - - +
108C ALA* 1.3 78.1 - - - +
110C ALA* 1.3 62.8 + - - +
234C GLN 6.2 0.2 - - - +
236C VAL* 4.1 20.1 - - + +
237C ASP* 2.8 43.1 + - - +
238C MET* 3.4 6.9 + - - +
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Residues in contact with ALA 110 (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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70C VAL* 3.7 13.9 - - + -
71C ALA 2.7 18.6 + - - +
72C ARG* 4.1 7.6 - - + -
73C LEU* 2.9 35.4 + - - +
109C VAL* 1.3 76.6 - - - +
111C LEU* 1.3 60.0 + - - +
112C ASP 4.1 0.2 - - - -
236C VAL* 5.2 0.4 - - - -
238C MET* 3.5 23.8 - - + -
240C PHE* 3.9 16.4 - - + -
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Residues in contact with LEU 111 (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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73C LEU* 4.0 3.1 - - + -
75C PHE* 3.6 36.1 - - + -
87C ILE* 6.5 0.4 - - + -
109C VAL 4.4 0.2 - - - -
110C ALA* 1.3 73.6 - - - +
112C ASP* 1.3 56.3 + - - +
113C THR* 3.6 29.4 - - + +
227C ASP* 3.4 28.3 - - + +
228C LEU* 4.6 13.0 - - + -
230C PHE* 4.6 1.3 - - + -
231C GLY* 4.0 18.8 - - - +
236C VAL* 4.4 12.8 - - + -
238C MET 3.3 14.2 + - - +
239C VAL* 3.3 8.3 - - + +
240C PHE* 2.8 31.1 + - - +
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Residues in contact with ASP 112 (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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72C ARG* 2.7 45.2 + - + +
73C LEU 2.9 18.2 + - - +
74C ASN* 3.9 4.9 - - - +
75C PHE* 3.0 28.4 + - - +
110C ALA 4.1 0.4 + - - -
111C LEU* 1.3 74.7 - - - +
113C THR* 1.3 69.3 + - - +
240C PHE* 3.4 25.6 - - + +
242C SER* 3.5 0.7 + - - -
269C LYS* 2.7 30.7 + - - -
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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