Contacts of the strand formed by residues 163 - 168 (chain F) in PDB entry 5ANC
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 GLN 163 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52F LEU* 3.8 17.7 - - + -
53F ILE 3.2 11.2 - - - +
54F SER* 3.9 8.0 - - - -
55F LEU* 3.6 11.3 - - - +
60F LEU* 5.4 1.2 - - - +
135F ILE* 3.3 23.8 - - - +
156F SER* 4.0 27.4 - - - +
159F PHE* 2.9 43.6 + - + +
160F PRO 3.0 13.4 + - - +
161F GLY 2.9 14.6 + - - +
162F ARG* 1.3 79.3 + - - +
164F LYS* 1.3 68.4 + - - +
1440N A 5.5 1.4 + - - +
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Residues in contact with LYS 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F LEU* 3.4 6.1 - - - +
53F ILE* 2.8 53.5 + - + +
55F LEU* 4.5 21.6 - - + +
163F GLN* 1.3 79.2 - - - +
165F ILE* 1.3 76.6 + - - +
166F VAL* 5.6 2.0 - - + +
1528N U 5.0 22.2 - - - +
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Residues in contact with ILE 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F VAL* 4.4 8.5 - - + -
51F HIS 3.3 12.6 - - - +
52F LEU* 4.0 9.9 - - + -
149F VAL* 3.9 28.9 - - + +
152F LEU* 3.5 43.7 - - + -
153F ARG* 4.4 6.3 - - - +
156F SER* 4.5 7.0 - - - +
164F LYS* 1.3 92.3 - - - +
166F VAL* 1.3 61.8 + - - +
167F VAL* 5.5 3.2 - - + +
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Residues in contact with VAL 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F VAL* 3.4 1.0 - - - -
51F HIS* 2.8 51.4 + - + +
53F ILE* 3.9 24.2 - - + -
134F ILE* 6.4 0.2 - - + -
164F LYS* 4.2 2.4 - - + +
165F ILE* 1.3 75.5 - - - +
167F VAL* 1.3 75.7 + - - +
168F SER* 3.6 4.3 + - - +
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Residues in contact with VAL 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F LEU* 4.3 20.0 - - + -
49F CYS 3.1 18.4 - - - +
50F VAL* 3.9 15.9 - - + +
149F VAL* 5.6 5.4 - - + -
165F ILE* 5.5 3.6 - - + +
166F VAL* 1.3 84.1 - - - +
168F SER* 1.3 69.7 + - - +
169F LYS* 3.8 2.4 + - - +
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Residues in contact with SER 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F LEU* 5.8 0.2 - - - +
49F CYS* 2.8 27.1 + - - +
51F HIS* 3.1 32.6 + - - -
166F VAL* 3.6 5.4 + - - +
167F VAL* 1.3 85.9 - - - +
169F LYS* 1.3 60.2 + - - +
170F LYS* 3.2 28.1 + - - +
178F ARG* 5.7 1.7 + - - -
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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