Contacts of the strand formed by residues 310 - 317 (chain B) in PDB entry 4Y5U
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 LEU 310 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PRO 3.7 4.6 + - - +
309B PRO* 1.3 74.9 - - - +
311B VAL* 1.3 63.7 + - - +
312B ARG* 3.8 2.5 + - - +
344B THR* 3.2 42.0 - - + +
345B VAL 3.6 8.7 - - - +
346B PRO* 4.1 24.7 - - + -
389B SER 3.6 8.1 - - - +
390B ALA* 3.8 7.0 - - - +
391B SER 5.0 1.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B PHE* 4.3 7.2 - - + -
293B VAL* 3.8 14.8 - - + -
310B LEU* 1.3 72.1 - - - +
312B ARG* 1.3 72.2 + - - +
343B ASN 3.5 1.0 - - - +
344B THR* 3.3 4.4 - - - -
345B VAL 2.7 37.6 + - - +
347B LEU* 3.9 35.2 - - + -
358B ALA* 4.2 7.6 - - + -
360B PHE* 3.6 18.0 - - + -
388B PHE* 4.3 3.4 - - + -
389B SER 3.4 14.4 - - - +
390B ALA* 3.5 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B LEU* 3.8 3.1 + - - +
311B VAL* 1.3 79.1 - - - +
313B ALA* 1.3 63.9 + - - +
314B ASP* 3.1 26.0 + - - +
343B ASN* 3.2 21.1 - - - +
344B THR* 3.8 22.7 - - + +
360B PHE* 4.5 0.4 - - - -
387B LEU 4.5 0.2 - - - -
388B PHE* 3.3 5.2 - - - +
389B SER* 3.0 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ARG* 1.3 74.3 - - - +
314B ASP* 1.3 68.7 + - - +
340B ILE* 4.0 11.0 - - + +
343B ASN* 2.8 38.3 + - + +
360B PHE* 4.1 15.9 - - + -
363B LEU* 4.8 7.9 - - + -
386B VAL* 4.2 14.4 - - + -
387B LEU 3.6 4.5 - - - -
388B PHE* 4.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ARG* 3.1 31.8 + - - +
313B ALA* 1.3 78.9 - - - +
315B MET* 1.3 66.0 + - - +
316B VAL* 3.5 8.5 - - + +
339B GLU 5.7 3.1 + - - -
340B ILE* 4.1 3.4 - - - -
343B ASN* 4.2 7.3 + - - -
386B VAL* 4.0 2.1 - - - +
387B LEU* 2.9 40.7 + - + +
389B SER* 5.8 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B LEU* 4.3 16.8 - - + -
289B PHE* 5.3 1.1 - - + -
314B ASP* 1.3 74.2 + - - +
316B VAL* 1.3 68.9 + - - +
320B GLN* 4.4 1.9 - - - +
339B GLU* 4.6 21.8 + - - +
340B ILE* 3.6 23.4 - - + +
365B LEU* 3.8 34.8 - - + -
384B CYS* 3.8 20.4 - - - -
385B ALA 3.2 28.9 - - - +
386B VAL* 4.3 13.5 - - + +
410B LEU* 4.3 3.8 - - + -
412B VAL* 4.4 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ASP* 3.5 12.3 - - + +
315B MET* 1.3 85.1 - - - +
317B THR* 1.3 67.8 + - - +
320B GLN* 3.5 22.4 - - + +
321B ALA* 4.4 8.1 - - + +
384B CYS* 3.0 23.1 - - - +
385B ALA* 2.7 37.1 + - + +
387B LEU* 4.1 18.6 - - + +
406B LEU* 4.2 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B VAL* 1.3 77.3 - - - +
318B GLU* 1.3 64.1 + - - +
319B LYS* 3.1 15.5 + - - +
320B GLN* 3.2 35.2 + - - +
321B ALA* 3.1 20.3 + - - +
383B LYS 4.6 1.1 - - - -
384B CYS* 4.2 8.1 - - + -
----------------------------------------------------------
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