Contacts of the helix formed by residues 264 - 268 (chain A) in PDB entry 2IG7
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 ASP 264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A GLY 5.3 2.6 - - - +
80A ASN* 6.2 0.7 - - - -
104A ARG* 3.4 39.0 + - - -
123A PHE* 5.8 6.0 - - - -
143A ARG* 4.4 4.3 + - - +
240A HIS* 3.1 17.5 + - - -
242A ASP* 4.9 2.6 - - - +
246A GLY 4.8 1.7 - - - +
247A ASN* 2.8 27.8 + - - +
263A VAL* 1.3 86.6 - - - +
265A PHE* 1.3 59.0 + - - +
266A GLU* 3.2 29.6 + - - +
267A TYR* 4.7 3.5 + - - -
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Residues in contact with PHE 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 3.7 7.3 - - - +
119A GLU* 5.3 1.6 - - - -
122A MSE 4.4 16.2 - - + +
126A LEU* 3.4 28.0 - - + -
174A PHE* 3.4 41.1 - + + -
238A PHE* 3.9 17.7 - + - -
240A HIS* 3.7 37.9 - + + -
262A LEU* 3.5 31.4 - - + -
263A VAL* 4.2 4.9 - - - -
264A ASP* 1.3 73.7 - - - +
266A GLU* 1.3 65.3 + - - +
267A TYR 3.2 3.1 - - - +
268A SER* 2.8 43.3 + - - +
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Residues in contact with GLU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ASN* 4.1 15.2 + - - +
104A ARG* 5.2 0.4 - - - -
106A TYR* 4.4 4.9 - - + -
110A LEU* 3.7 35.9 - - + +
115A SER* 5.3 3.8 + - - +
118A LEU* 4.2 9.6 - - - +
119A GLU* 3.3 37.1 - - + +
123A PHE* 5.3 0.3 - - - +
143A ARG* 2.9 36.7 + - - -
264A ASP* 3.2 30.3 + - - +
265A PHE* 1.3 80.4 + - - +
267A TYR* 1.3 66.6 + - + +
268A SER 3.4 1.2 + - - -
1004A UNX 4.0 5.7 - - - -
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Residues in contact with TYR 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A SER* 2.7 31.9 + - - -
109A ILE* 3.6 11.9 - - + +
110A LEU* 3.8 25.6 - - + +
187A TRP* 3.5 11.5 + - + -
195A TYR* 4.2 8.3 - - - -
240A HIS 3.5 10.7 + - - +
241A ASN* 2.9 29.0 + - + +
242A ASP* 4.2 18.4 - - + -
264A ASP 4.7 2.3 + - - -
265A PHE 3.2 0.8 - - - -
266A GLU* 1.3 81.3 - - + +
268A SER* 1.3 62.9 + - - +
352A PHE* 4.6 10.1 - + - -
353A TRP* 4.0 22.2 - + + -
356A TRP* 2.9 34.2 + + - -
1004A UNX 3.8 15.0 - - - -
1007A UNX 4.0 9.0 - - - -
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Residues in contact with SER 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 3.3 22.5 - - - +
122A MSE 3.8 2.8 - - - +
187A TRP* 4.7 0.9 + - - -
238A PHE* 3.4 23.4 - - - -
239A CYS 3.1 17.3 - - - -
240A HIS 3.3 7.4 + - - -
265A PHE* 2.8 38.0 + - - +
266A GLU 3.4 1.1 - - - +
267A TYR* 1.3 79.6 - - - +
269A SER* 1.3 73.6 + - - +
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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