Contacts of the strand formed by residues 222 - 225 (chain G) in PDB entry 3EXF
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 GLY 222 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14G LEU* 3.6 1.9 - - - -
15G HIS* 2.9 34.6 + - - +
17G LEU* 3.6 7.4 - - - +
214G TYR* 3.7 18.2 - - - -
221G PRO* 1.3 72.9 - - - +
223G LEU* 1.3 63.4 + - - +
251G ILE* 4.5 2.2 - - - -
252G LEU 2.7 19.3 - - - -
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Residues in contact with LEU 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G CYS* 3.8 16.2 - - + -
13G ASP 3.1 10.1 - - - +
14G LEU* 4.2 7.4 - - + -
17G LEU* 4.7 0.7 - - + -
21G PRO* 3.5 34.5 - - + -
214G TYR* 3.8 6.5 - - - +
222G GLY* 1.3 74.7 - - - +
224G ARG* 1.3 61.3 + - - +
225G VAL* 4.0 9.5 + - + +
236G ALA* 4.1 10.8 - - + -
239G PHE* 3.8 13.9 - - + -
240G ALA* 4.7 2.2 - - + -
251G ILE* 3.5 30.3 - - + -
252G LEU 2.8 11.3 + - - +
253G MET* 3.4 20.8 - - + -
254G GLU 3.1 22.2 + - - -
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Residues in contact with ARG 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G LYS* 6.1 0.5 - - - +
11G LYS 5.0 0.2 - - - +
12G CYS* 3.3 23.7 - - - +
13G ASP* 3.0 44.9 + - + +
211G THR 4.5 4.0 + - - -
212G ASP* 3.6 26.9 + - - +
214G TYR* 3.8 22.7 + - + -
223G LEU* 1.3 72.4 - - - +
225G VAL* 1.3 60.8 + - - +
226G ASP 4.4 0.2 + - - -
254G GLU* 3.4 41.3 + - - +
256G GLN* 3.5 31.9 + - - +
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Residues in contact with VAL 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G CYS* 3.8 13.7 - - - -
223G LEU* 4.0 12.8 - - + +
224G ARG* 1.3 80.5 - - - +
226G ASP* 1.3 58.6 - - - +
227G GLY* 2.7 17.8 + - - -
232G CYS* 3.7 35.7 - - + +
233G VAL* 4.3 5.2 - - + +
236G ALA* 3.6 22.9 - - + -
253G MET* 4.1 13.5 - - + -
254G GLU 2.8 13.9 + - - +
255G LEU* 3.8 11.4 - - + -
256G GLN* 2.9 24.6 + - - +
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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