Contacts of the strand formed by residues 313 - 320 (chain B) in PDB entry 4RUH
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 313 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A SER 4.5 0.7 + - - -
233A GLY* 3.6 26.0 + - - -
234A GLY* 3.8 6.7 - - - -
211B ARG* 3.1 29.6 + - - +
257B ILE* 4.2 6.3 - - - -
312B PRO* 1.3 77.5 - - - +
314B LEU* 1.3 61.9 + - - +
315B SER* 5.1 1.0 + - - -
342B ILE* 3.2 7.3 - - - +
343B ARG* 2.8 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLU* 4.2 7.6 - - - +
241A THR* 5.2 4.4 + - - +
250B LEU* 4.0 25.1 - - + +
251B VAL* 4.0 18.2 - - + +
257B ILE* 3.7 41.8 - - + +
259B ILE* 4.6 2.5 - - + -
313B SER* 1.3 77.2 - - - +
315B SER* 1.3 69.7 + - - +
316B LEU* 3.8 30.2 + - + -
340B PHE* 4.2 9.0 - - + -
341B SER 3.2 10.5 - - - +
342B ILE* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A SER* 3.9 22.4 + - - -
233A GLY* 4.4 3.5 - - - -
238A GLU* 2.7 30.7 + - - -
332A ILE* 4.0 2.9 - - - +
313B SER* 4.3 1.8 + - - -
314B LEU* 1.3 75.7 + - - +
316B LEU* 1.3 63.2 + - - +
317B HIS* 3.7 23.9 + - - -
340B PHE* 3.2 6.8 - - - +
341B SER* 2.9 33.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLU* 3.8 8.5 + - - +
240A MET* 3.1 31.8 - - + +
241A THR* 4.0 30.0 + - - +
244A ILE* 4.0 32.8 - - + -
331A VAL 4.7 0.7 - - - +
332A ILE* 5.7 0.2 - - - -
333A PRO* 4.5 4.3 - - - +
247B MET* 3.9 24.0 - - + +
250B LEU* 3.8 23.8 - - + -
251B VAL* 4.7 7.4 - - + -
314B LEU* 3.8 13.4 + - + -
315B SER* 1.3 71.2 - - - +
317B HIS* 1.3 60.0 + - - +
318B GLY 3.7 0.7 - - - -
339B LYS 4.0 0.2 - - - -
340B PHE* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A SER* 3.5 20.0 - - - -
240A MET* 4.5 0.9 - - - -
322A ALA* 3.6 6.0 - - - +
323A PHE* 3.0 30.4 + - + +
329A LYS 3.3 11.9 - - - +
330A THR* 3.7 2.2 - - - -
331A VAL 3.0 33.3 + - - +
333A PRO* 3.7 7.3 - - - +
215B TYR* 3.3 36.5 - + - +
315B SER* 3.8 14.9 + - - -
316B LEU* 1.3 76.0 - - - +
318B GLY* 1.3 59.4 + - - +
339B LYS* 2.9 11.6 + - + +
340B PHE* 3.6 19.7 - - - -
341B SER* 2.8 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A MET* 4.1 10.4 - - - +
319A ILE* 5.6 0.2 - - - -
322A ALA* 3.9 12.6 - - - -
323A PHE 3.4 12.8 - - - -
247B MET* 4.3 3.4 - - - +
316B LEU 3.7 1.2 - - - -
317B HIS* 1.3 82.4 - - - +
319B ILE* 1.3 64.2 + - - +
320B GLU 4.3 0.2 - - - -
338B GLY* 3.6 2.4 - - - -
339B LYS* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ILE* 4.0 25.2 - - + +
322A ALA* 5.1 2.0 - - - +
323A PHE 3.5 5.4 + - - -
324A SER* 3.4 22.0 - - - -
240B MET* 3.8 20.0 - - + -
243B LEU* 3.8 33.0 - - + -
244B ILE* 3.8 21.3 - - + -
247B MET* 4.1 11.4 - - + -
318B GLY* 1.3 80.7 - - - +
320B GLU* 1.3 74.6 + - - +
321B GLY 4.1 0.5 + - - -
322B ALA* 4.1 17.2 + - + +
324B SER* 5.3 1.6 - - - -
336B VAL* 3.8 9.4 - - + -
337B VAL 3.3 3.4 - - - +
338B GLY* 4.4 0.2 - - - -
339B LYS* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A SER* 3.6 17.5 - - - +
325A GLY 3.5 4.0 - - - +
326A SER* 3.3 23.6 + - - -
327A GLY 4.3 0.9 + - - -
319B ILE* 1.3 75.3 - - - +
321B GLY* 1.3 63.9 + - - +
322B ALA 3.4 0.2 - - - -
335B LYS 4.0 0.2 - - - +
336B VAL* 3.3 5.2 - - - -
337B VAL* 2.7 52.1 + - + +
339B LYS* 2.7 41.8 + - - +
----------------------------------------------------------
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