Contacts of the strand formed by residues 222 - 226 (chain Q) in PDB entry 3EXG
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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14Q LEU* 3.7 0.3 - - - -
15Q HIS* 3.0 31.9 + - - +
17Q LEU* 3.6 7.6 - - - +
214Q TYR* 3.6 24.9 - - - -
220Q ILE 3.5 1.2 + - - -
221Q PRO* 1.3 74.2 - - - +
223Q LEU* 1.3 66.6 + - - +
251Q ILE* 4.5 0.2 - - - +
252Q LEU 2.9 12.6 - - - -
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Residues in contact with LEU 223 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Q CYS* 4.2 6.3 - - + -
13Q ASP 3.2 11.0 - - - +
14Q LEU* 3.8 9.0 - - + -
17Q LEU* 4.6 1.3 - - + -
21Q PRO* 3.6 33.7 - - + -
214Q TYR* 3.8 6.5 - - - +
222Q GLY* 1.3 75.2 - - - +
224Q ARG* 1.3 60.6 + - - +
225Q VAL* 3.6 3.5 + - + -
236Q ALA* 4.2 14.1 - - + +
239Q PHE* 3.7 17.7 - - + -
240Q ALA* 5.2 0.7 - - + -
251Q ILE* 3.5 25.8 - - + -
252Q LEU 3.1 15.7 + - - +
253Q MET* 3.3 23.0 - - + +
254Q GLU 3.0 22.5 + - - -
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Residues in contact with ARG 224 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Q LYS* 5.6 2.9 - - - +
12Q CYS* 3.4 23.1 - - - -
13Q ASP* 3.0 41.8 + - + +
211Q THR 4.8 6.7 + - - -
212Q ASP* 4.2 16.4 + - - +
214Q TYR* 3.6 30.6 + - + -
223Q LEU* 1.3 69.7 - - - +
225Q VAL* 1.3 62.6 + - - +
254Q GLU* 3.1 37.1 + - - +
256Q GLN* 3.6 34.4 + - - +
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Residues in contact with VAL 225 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Q LYS* 5.7 1.1 - - - -
12Q CYS* 3.5 17.3 - - - -
223Q LEU* 4.2 5.6 - - + +
224Q ARG* 1.3 75.0 - - - +
226Q ASP* 1.3 75.8 + - - +
227Q GLY 3.8 0.2 - - - -
232Q CYS* 3.8 17.3 - - + -
233Q VAL* 4.2 7.4 - - + +
236Q ALA* 3.4 29.6 - - + -
253Q MET* 4.1 16.2 - - + -
254Q GLU 2.8 13.8 + - - +
255Q LEU* 4.0 16.8 - - + -
256Q GLN* 3.1 32.2 + - - +
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Residues in contact with ASP 226 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Q LYS* 4.3 32.1 + - + +
12Q CYS* 5.5 0.4 - - - -
225Q VAL* 1.3 85.0 - - - +
227Q GLY* 1.3 63.1 + - - +
228Q MET* 3.1 23.5 + - - +
229Q ASP* 3.6 22.9 + - - +
232Q CYS* 3.7 20.1 - - - +
233Q VAL* 3.7 6.9 - - - +
256Q GLN* 4.0 8.1 - - - +
290Q LEU* 5.8 1.6 - - - +
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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