Contacts of the strand formed by residues 10 - 14 (chain F) in PDB entry 4GG6
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 HIS 10 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8F PRO* 3.8 15.2 - - - +
9F LYS* 1.3 92.2 + - + +
11F LEU* 1.3 64.8 + - - +
12F ILE* 6.2 0.2 - - + -
123F ARG* 3.6 34.0 + - + -
167F HIS* 3.8 19.1 - - + +
168F VAL 5.4 0.4 + - - -
169F GLU* 5.3 5.1 - - - +
228F TYR* 3.4 68.5 - + + +
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Residues in contact with LEU 11 (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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8F PRO* 3.8 18.6 - - + -
10F HIS* 1.3 77.2 - - - +
12F ILE* 1.3 75.3 + - - +
13F THR* 3.6 33.2 - - + +
19F VAL* 4.0 23.1 - - + -
20F THR 5.4 1.1 - - - +
21F LEU* 3.8 28.5 - - + -
122F THR* 4.1 6.5 - - + -
123F ARG 2.8 14.6 + - - +
124F LEU* 3.3 11.6 - - + -
125F THR 3.0 24.9 + - - +
167F HIS* 3.3 4.8 + - - -
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Residues in contact with ILE 12 (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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10F HIS* 6.4 0.2 - - + -
11F LEU* 1.3 82.0 - - - +
13F THR* 1.3 72.5 + - - +
125F THR* 3.6 10.5 - - + +
127F THR* 4.4 15.3 - - + -
130F LEU* 4.3 10.1 - - + +
133F VAL* 4.3 24.5 - - + -
164F TYR* 5.6 0.7 - - + -
165F PRO* 3.8 29.4 - - + -
167F HIS* 4.0 12.1 - - + +
228F TYR 3.5 24.5 - - - +
229F GLY* 3.9 22.9 - - - +
230F LEU* 4.6 11.7 - - + +
234F ASP* 5.7 0.9 - - - +
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Residues in contact with THR 13 (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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11F LEU* 3.6 15.7 - - + +
12F ILE* 1.3 79.3 - - - +
14F ALA* 1.3 69.6 - - - +
17F GLN* 4.6 10.1 - - + +
19F VAL* 3.7 23.1 - - + +
94F LEU* 3.5 22.5 - - - +
124F LEU* 3.6 5.7 - - - +
125F THR 3.2 5.1 + - - -
126F VAL* 3.3 8.0 - - - +
127F THR* 3.1 24.1 + - - +
130F LEU* 3.9 9.9 - - + -
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Residues in contact with ALA 14 (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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13F THR* 1.3 79.8 - - - +
15F THR* 1.3 68.2 + - - +
17F GLN* 3.2 32.3 + - + +
94F LEU* 4.2 2.3 - - - +
126F VAL* 4.0 5.1 - - - +
127F THR* 3.6 9.2 - - - +
128F GLU 5.1 4.5 - - - +
129F ASP* 5.5 0.4 - - - -
130F LEU* 3.7 27.0 - - + +
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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