Contacts of the strand formed by residues 311 - 319 (chain B) in PDB entry 1C3B
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 SER 311 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ARG* 3.0 26.4 + - - -
273B MET* 4.5 6.9 - - - +
274B LEU 3.3 9.6 - - - -
276B TRP* 4.0 5.6 - - - +
308B VAL* 2.7 24.2 + - - +
309B ARG 3.0 4.4 + - - -
310B ALA* 1.3 76.5 - - - +
312B TRP* 1.3 61.2 + - - +
313B VAL* 3.7 17.9 - - - -
329B ILE* 3.1 28.8 - - - +
330B PRO* 3.4 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B MET* 3.4 2.9 - - - -
274B LEU* 2.7 46.3 + - + +
276B TRP* 3.5 37.1 - + + +
278B VAL* 4.1 17.0 - - + -
283B ILE* 3.9 20.7 - - + +
311B SER* 1.3 71.9 - - - +
313B VAL* 1.3 59.0 + - - +
314B HIS* 3.4 35.8 + + + +
325B TYR* 3.5 18.3 + + - -
327B ALA* 3.6 14.4 - - + -
328B PHE 3.6 3.6 - - - -
329B ILE* 4.0 12.3 - - + -
350B VAL* 5.1 1.1 - - + -
353B ALA* 4.4 4.3 - - + -
354B TRP* 4.1 33.0 - + - -
357B LEU* 3.9 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B GLN* 4.4 9.6 - - - +
271B TRP* 3.9 22.2 - - + -
272B GLU 3.6 10.1 - - - +
273B MET* 3.9 15.3 - - + -
308B VAL 5.5 0.2 - - - +
311B SER* 3.8 19.7 - - - -
312B TRP* 1.3 75.5 - - - +
314B HIS* 1.3 64.7 + - - +
327B ALA* 3.1 3.6 - - - +
328B PHE* 2.7 79.1 + - + +
330B PRO* 3.9 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B MET* 6.0 0.6 - - - +
271B TRP* 3.9 9.0 - - - -
272B GLU* 3.1 53.7 + - + +
274B LEU* 3.8 19.7 - - + +
283B ILE* 4.7 16.2 - - + -
287B SER* 5.8 3.1 - - - -
312B TRP* 3.4 24.6 + + - +
313B VAL* 1.3 77.0 - - - +
315B LYS* 1.3 67.9 + - - +
316B THR* 5.8 2.9 - - + -
325B TYR* 3.0 29.8 + + - +
326B VAL 3.0 15.7 - - - +
327B ALA* 3.9 1.8 - - + +
350B VAL* 5.4 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER* 3.3 25.2 + - - +
65B VAL* 3.5 14.4 - - + +
67B LYS* 3.6 9.0 - - + +
68B THR* 3.8 23.6 - - + -
112B TYR* 4.7 0.4 + - - -
150B TYR* 2.9 32.2 + - - -
270B GLY 3.4 22.4 - - - +
271B TRP* 4.4 3.6 - - + -
272B GLU* 3.5 24.7 - - - +
314B HIS* 1.3 84.9 - - - +
316B THR* 1.3 82.2 + - - +
325B TYR* 3.5 4.4 - - - -
326B VAL* 3.0 27.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER* 3.7 3.6 - - - -
65B VAL* 3.9 2.2 - - - -
150B TYR* 4.7 0.2 + - - -
287B SER* 4.9 6.1 - - - -
314B HIS* 5.6 3.1 - - + +
315B LYS* 1.3 103.9 + - - +
317B GLY* 1.3 60.2 + - - +
324B SER 3.8 4.7 - - - -
325B TYR* 3.4 27.8 - - + -
346B ASN* 3.7 35.4 + - + +
349B ARG* 4.3 3.8 - - - +
350B VAL* 4.5 9.4 - - + -
362B BZB 4.6 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU 3.5 20.9 - - - -
64B SER 3.6 9.2 - - - -
65B VAL* 3.8 3.2 - - - +
316B THR* 1.3 77.0 - - - +
318B ALA* 1.3 61.6 + - - -
324B SER* 3.0 21.5 + - - -
349B ARG* 2.7 21.8 + - - -
362B BZB 3.7 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU 4.9 0.7 - - - -
63B GLY* 3.6 4.9 - - - +
64B SER 3.7 2.6 - - - +
317B GLY* 1.3 77.9 - - - +
319B THR* 1.3 69.8 + - - +
322B PHE 3.2 14.1 - - - +
343B ASN* 3.6 24.2 - - - +
346B ASN* 5.6 0.7 - - - +
349B ARG* 4.0 5.2 - - - +
362B BZB 2.8 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLU* 2.8 30.4 + - + +
63B GLY* 3.5 23.6 - - - +
211B VAL* 4.0 22.2 - - + -
221B TYR* 4.7 7.6 - - + +
318B ALA* 1.3 79.9 - - - +
320B GLY* 1.3 67.8 + - - +
321B GLY 3.2 1.3 + - - -
322B PHE* 3.0 28.3 + - + +
343B ASN* 3.0 20.0 + - - -
362B BZB 5.6 0.9 - - - -
----------------------------------------------------------
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