Contacts of the helix formed by residues 312 - 316 (chain A) in PDB entry 2ID5
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 GLU 312 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A VAL 5.2 3.2 + - - +
289A PRO* 3.7 22.6 - - + +
310A THR* 4.0 12.7 - - - +
311A LEU* 1.3 75.8 - - - +
313A GLU* 1.3 65.4 + - - +
314A SER* 3.8 14.6 + - - +
315A VAL* 3.1 35.2 + - + +
337A ARG* 3.5 35.4 - - + +
340A TRP* 3.8 3.3 - - - +
463A ALA* 5.2 2.1 - - - +
122D TYR* 5.7 1.6 - - - -
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU* 1.3 73.1 - - - +
314A SER* 1.3 57.3 + - - +
315A VAL 3.1 1.8 + - - -
316A PHE* 3.2 14.9 + - - +
319A VAL* 4.0 23.4 - - + +
337A ARG 4.7 0.6 + - - -
340A TRP* 3.3 55.4 - - + +
344A ARG* 4.2 2.9 + - - -
97D LEU* 5.4 6.1 - - - +
125D GLN* 2.7 40.0 + - - +
126D ASP* 2.9 40.5 - - - +
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Residues in contact with SER 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A PRO* 3.4 21.5 - - - +
290A TYR* 3.1 24.7 + - - -
312A GLU* 3.8 13.9 + - - +
313A GLU* 1.3 75.3 - - - +
315A VAL* 1.3 63.5 + - - +
316A PHE 3.1 7.1 + - - +
122D TYR* 3.8 42.7 - - - -
125D GLN* 3.5 12.7 + - - +
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Residues in contact with VAL 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A VAL* 3.4 39.9 - - + +
288A GLU 3.4 15.7 - - - +
289A PRO* 4.0 2.9 - - + -
290A TYR* 3.6 9.0 - - - +
291A ALA* 3.8 0.9 + - + -
292A PHE* 3.0 42.3 + - + +
311A LEU* 4.4 6.3 - - + -
312A GLU* 3.1 25.4 - - + +
313A GLU 3.1 1.2 - - - -
314A SER* 1.3 78.1 - - - +
316A PHE* 1.3 91.6 + - + +
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Residues in contact with PHE 316 (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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290A TYR* 5.7 2.1 - - - -
292A PHE* 4.0 15.7 - + + -
293A ARG* 5.1 3.2 + - - -
298A LEU* 4.2 15.7 - - + -
301A LEU* 3.6 31.0 - - + -
311A LEU* 3.7 11.7 - - + -
312A GLU 4.3 0.9 - - - -
313A GLU 3.2 13.3 + - - +
314A SER 3.1 5.7 - - - +
315A VAL* 1.3 97.8 - - + +
317A HIS* 1.3 65.4 + - - +
318A SER 4.4 3.4 - - - +
319A VAL* 4.3 20.2 - - + +
322A LEU* 3.6 38.4 - - + -
325A LEU* 4.0 1.8 - - + -
340A TRP* 3.6 29.8 - + - -
125D GLN* 3.6 15.2 + - - -
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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