Contacts of the helix formed by residues 171 - 175 (chain Q) in PDB entry 2JA7
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 LYS 171 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1224N PHE* 3.3 41.7 - - + +
165Q LEU* 4.6 2.2 - - - -
169Q ARG* 4.2 15.7 + - - +
170Q LEU* 1.3 84.6 + - - +
172Q GLU* 1.3 68.8 + - - +
173Q SER* 2.9 15.0 + - - +
174Q GLN* 3.0 31.3 + - - +
175Q LEU* 3.9 3.1 + - - +
140R ASP* 4.7 15.8 + - - +
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Residues in contact with GLU 172 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161Q LYS* 2.6 38.7 + - - -
165Q LEU* 4.2 18.0 - - + +
171Q LYS* 1.3 71.4 - - - +
173Q SER* 1.3 61.9 + - - +
175Q LEU* 3.2 25.6 - - + +
193Q GLY* 5.2 2.3 - - - -
213Q ILE* 3.2 33.1 - - + +
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Residues in contact with SER 173 (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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862M ASN* 4.1 8.2 + - - -
1224N PHE* 5.4 5.0 - - - -
171Q LYS* 2.9 12.0 + - - +
172Q GLU* 1.3 73.0 - - - +
174Q GLN* 1.3 62.4 + - - +
175Q LEU 2.8 19.6 + - - +
177Q ARG* 3.7 29.4 + - - +
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Residues in contact with GLN 174 (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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857M ARG* 4.4 6.7 + - - +
860M LEU 2.9 22.8 + - - +
861M GLY* 3.3 25.6 + - - +
862M ASN* 3.3 27.6 - - - +
863M VAL* 3.0 26.1 + - - +
1422M ARG* 5.9 1.6 - - - +
1224N PHE* 5.1 9.7 + - + -
169Q ARG 4.4 3.1 - - - +
170Q LEU* 3.7 13.5 - - + -
171Q LYS* 3.0 44.9 + - - +
173Q SER* 1.3 80.7 - - - +
175Q LEU* 1.3 59.1 + - - +
176Q PRO* 3.8 2.8 - - - +
139R PRO 5.4 5.3 + - - -
140R ASP* 6.2 0.8 - - - +
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Residues in contact with LEU 175 (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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866M PHE* 4.2 7.6 - - + -
161Q LYS* 6.3 0.4 - - - -
164Q LEU* 4.3 10.8 - - + -
165Q LEU* 3.4 29.2 - - + -
170Q LEU* 4.2 15.7 - - + -
171Q LYS 3.9 2.1 + - - +
172Q GLU* 3.2 17.5 - - + +
173Q SER 2.8 8.6 + - - +
174Q GLN* 1.3 78.3 - - - +
176Q PRO* 1.3 87.2 - - + +
177Q ARG* 3.3 15.9 + - - +
195Q VAL* 4.8 7.2 - - + -
211Q TYR* 3.9 29.2 - - + +
212Q ARG 5.0 0.2 - - - +
213Q ILE* 4.0 23.6 - - + +
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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