Contacts of the helix formed by residues 312 - 316 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B VAL 5.3 2.3 + - - +
289B PRO* 4.4 21.3 - - + +
310B THR* 4.2 18.4 - - + +
311B LEU* 1.3 73.9 - - - +
313B GLU* 1.3 66.2 + - - +
314B SER* 3.2 12.4 + - - +
315B VAL* 3.0 32.9 + - + +
337B ARG* 3.3 36.2 - - + +
340B TRP* 4.2 2.5 - - - +
463B ALA* 5.4 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A THR* 5.3 2.1 - - - +
125A GLN* 3.9 23.9 - - + +
126A ASP* 2.4 45.1 + - - +
312B GLU* 1.3 74.0 - - - +
314B SER* 1.3 60.7 + - - +
315B VAL 3.1 1.8 + - - -
316B PHE* 3.2 22.0 + - - +
319B VAL* 3.8 22.9 - - + +
340B TRP* 3.5 51.0 - - + +
344B ARG* 3.5 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR* 3.6 39.6 - - - -
125A GLN* 3.8 18.9 - - - +
289B PRO* 3.3 21.5 - - - +
290B TYR* 2.9 26.3 + - - -
293B ARG* 5.7 0.2 - - - -
312B GLU* 4.3 8.8 + - - +
313B GLU* 1.3 75.3 - - - +
315B VAL* 1.3 64.7 + - - +
316B PHE 3.0 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B VAL* 3.5 32.8 - - + +
288B GLU 3.6 14.6 - - - +
289B PRO* 3.9 2.9 - - + -
290B TYR 3.4 8.4 - - - +
291B ALA* 3.7 2.2 + - + -
292B PHE* 2.9 40.7 + - + +
293B ARG 3.9 0.2 + - - -
311B LEU* 4.3 11.9 - - + -
312B GLU* 3.0 24.9 - - + +
313B GLU 3.1 1.0 - - - -
314B SER* 1.3 78.7 + - - +
316B PHE* 1.3 96.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLN* 4.2 7.3 - - - +
290B TYR* 5.7 0.2 - - - -
292B PHE* 3.9 18.8 - + - -
293B ARG* 5.1 4.8 + - - -
298B LEU* 4.1 14.1 - - + -
301B LEU* 3.7 32.8 - - + -
311B LEU* 3.7 13.5 - - + -
313B GLU 3.2 18.4 + - - +
314B SER* 3.0 11.2 - - - +
315B VAL* 1.3 94.4 - - + +
317B HIS* 1.3 62.4 + - - +
318B SER 4.3 8.5 - - - +
319B VAL* 4.4 15.0 - - + +
322B LEU* 4.0 33.0 - - + -
325B LEU* 4.3 2.7 - - + -
340B TRP* 3.5 32.8 - + - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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