Contacts of the strand formed by residues 337 - 345 (chain B) in PDB entry 5INQ
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 337 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 4.4 9.2 - - + -
230B PHE* 4.6 0.2 - - + -
266B THR* 3.8 26.0 - - + +
268B ILE* 3.9 8.1 - - + -
296B PHE* 5.1 2.8 - - - -
330B PHE* 3.7 46.8 - - + -
332B ALA* 3.7 18.0 - - + +
335B GLY* 4.4 3.8 - - - -
336B HIS* 1.3 78.7 - - - +
338B ILE* 1.3 64.9 + - - +
339B PRO* 3.7 7.2 - - - +
366B LEU* 3.8 34.3 - - + -
367B ASN 3.6 12.6 - - - +
368B VAL* 4.3 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B PHE* 4.0 19.5 - - + -
335B GLY* 3.2 24.5 - - - +
337B LEU* 1.3 77.6 - - - +
339B PRO* 1.3 74.0 - - - +
340B GLN* 3.2 23.5 + - - +
366B LEU* 4.2 2.0 - - - -
367B ASN 3.0 33.7 + - - +
369B VAL* 3.2 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ALA* 4.2 10.1 - - + -
296B PHE* 3.6 24.7 - - + -
297B LEU* 3.5 35.2 - - + +
330B PHE* 3.6 30.7 - - + -
337B LEU 3.7 8.3 - - - +
338B ILE* 1.3 94.8 - - - +
340B GLN* 1.3 61.6 + - - +
364B CYS* 5.0 2.2 - - - -
365B THR 3.9 5.8 - - - +
366B LEU* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LEU* 4.1 10.6 - - - +
338B ILE* 3.2 40.0 + - - +
339B PRO* 1.3 74.6 + - - +
341B SER* 1.3 60.0 + - - +
365B THR* 2.8 22.8 + - - +
366B LEU* 4.2 0.9 - - - -
367B ASN* 3.1 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LEU* 3.9 6.9 - - - +
339B PRO 3.9 0.4 - - - -
340B GLN* 1.3 79.8 - - - +
342B LEU* 1.3 64.7 + - - +
343B ASP* 4.1 13.3 + - - -
363B LEU* 4.3 2.3 + - - +
364B CYS* 3.4 9.7 - - - -
365B THR* 2.6 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ALA* 4.8 1.1 - - + -
294B TRP* 3.9 37.7 - - + +
297B LEU* 3.6 16.8 - - + +
300B PRO* 5.2 1.9 - - + +
302B HIS* 3.1 19.1 + - - -
303B CYS* 3.7 25.2 - - - -
328B ILE* 3.7 28.9 - - + -
341B SER* 1.3 77.3 - - - +
343B ASP* 1.3 70.1 + - - +
362B LEU* 4.1 23.6 - - + -
363B LEU 3.3 15.0 - - - +
364B CYS* 3.8 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B HIS* 3.5 15.2 + - - -
303B CYS* 4.3 7.2 - - - -
341B SER* 4.1 12.1 + - - -
342B LEU* 1.3 88.4 + - - +
344B LEU* 1.3 68.3 + - - +
345B VAL* 5.4 0.4 - - + -
362B LEU* 3.5 4.8 - - - -
363B LEU* 2.8 54.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B TYR* 5.2 1.2 + - - -
302B HIS* 3.4 22.0 - - - +
303B CYS* 3.6 22.2 - - - +
305B TYR 3.8 16.6 - - - +
306B THR* 4.1 4.7 - - + -
343B ASP* 1.3 78.9 - - - +
345B VAL* 1.3 65.6 + - - +
347B LEU* 3.9 33.7 - - + +
360B TRP* 3.8 30.7 - - + +
361B GLY 3.2 6.3 - - - +
362B LEU* 3.7 24.7 - - + -
402B EPE 4.6 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 4.4 17.5 - - + -
129B TRP* 4.5 3.8 - - + -
149B CYS* 3.7 13.9 - - - -
153B TYR* 3.4 33.0 - - + +
343B ASP* 4.9 1.1 - - + -
344B LEU* 1.3 79.5 - - - +
346B GLY* 1.3 65.3 + - - +
347B LEU* 3.4 2.5 - - - -
360B TRP* 3.7 7.8 - - - +
361B GLY* 2.9 49.3 + - - -
362B LEU 4.2 1.1 - - - +
363B LEU* 3.9 21.8 - - + +
402B EPE 3.4 12.1 - - - +
----------------------------------------------------------
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