Contacts of the strand formed by residues 251 - 260 (chain A) in PDB entry 5FWV
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 HIS 251 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ALA* 4.0 1.6 - - - +
250A SER* 1.3 107.4 + - - +
252A ILE* 1.4 65.0 + - - +
253A HIS* 5.6 0.2 - - + -
293A ASN* 3.8 36.2 + - + +
294A VAL 3.2 17.7 - - - +
295A SER* 3.9 11.2 - - - +
296A LEU 3.8 4.9 - - - -
321A VAL* 3.1 55.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ILE* 4.5 17.5 - - + +
246A VAL* 4.8 6.5 - - + -
249A ALA* 4.4 2.7 - - + -
251A HIS* 1.4 76.3 - - - +
253A HIS* 1.3 65.7 + - - +
254A PHE* 3.5 30.0 - - + -
293A ASN* 3.5 3.8 - - - -
294A VAL* 2.8 40.4 + - + +
296A LEU 3.4 20.0 - - - +
297A ASP* 4.0 19.7 - - - +
298A PHE 4.4 1.3 - - - +
299A VAL* 4.4 11.9 - - + -
318A TYR* 4.1 15.0 - - + -
319A GLN 3.6 10.5 - - - +
320A ALA* 4.2 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A HIS* 5.0 0.4 + - - -
252A ILE* 1.3 72.9 - - - +
254A PHE* 1.3 65.0 + - - +
255A SER* 4.7 9.1 + - - -
291A SER* 2.2 36.8 + - - -
292A PHE 3.5 4.5 - - - -
293A ASN* 3.2 26.5 - - - +
317A LEU 3.7 1.1 + - - +
318A TYR* 3.2 5.5 - - - -
319A GLN* 2.8 64.7 + - + +
321A VAL* 5.3 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ILE* 4.1 21.3 - - + -
252A ILE* 3.5 34.1 - - + -
253A HIS* 1.3 80.0 - - - +
255A SER* 1.3 59.6 + - - +
256A PHE* 4.7 5.3 - + + -
270A LEU* 3.7 32.3 - - + -
291A SER* 3.2 6.4 + - - -
292A PHE* 2.8 65.7 + + + +
294A VAL* 3.9 8.3 - - + -
299A VAL* 4.2 16.8 - - + -
301A LEU* 5.1 3.1 - - + -
316A VAL* 3.8 22.4 - - + -
317A LEU 3.5 1.8 - - - -
318A TYR* 4.0 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A HIS* 4.7 9.1 + - - -
254A PHE* 1.3 75.2 - - - +
256A PHE* 1.3 68.3 + - - +
257A PRO* 3.4 5.1 - - - +
290A LEU 3.5 20.2 - - - -
291A SER* 4.4 4.9 - - - +
316A VAL* 3.4 7.1 - - - +
317A LEU* 2.9 52.1 + - - +
319A GLN* 5.3 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A PHE* 4.7 2.9 - - + -
255A SER* 1.3 84.1 - - - +
257A PRO* 1.3 59.8 - - - +
258A LEU* 2.9 18.8 + - - +
259A PHE* 3.9 28.3 + + + +
268A VAL* 4.7 14.6 - - + -
270A LEU* 5.1 8.3 - - + -
282A PHE* 4.0 25.6 - + - -
288A PRO* 3.4 36.1 - - + +
289A PRO 4.6 6.1 + - - +
290A LEU 4.5 3.8 + - - -
292A PHE* 4.2 14.6 - + - -
301A LEU* 5.4 0.2 - - + -
314A PHE* 4.8 4.7 - + - -
315A ALA 3.5 6.3 - - - -
316A VAL* 3.7 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.6 54.6 - - + +
39A ASP* 4.6 6.4 - - - +
224A VAL* 5.7 0.2 - - + -
255A SER* 3.4 16.2 - - - +
256A PHE* 1.3 84.7 - - - +
258A LEU* 1.3 60.1 + - - +
315A ALA 3.2 15.0 - - - +
316A VAL 5.2 0.2 - - - -
317A LEU* 4.2 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.7 13.9 - - + +
34A THR* 4.6 10.3 - - + -
39A ASP* 5.2 9.4 - - + +
230A PHE* 3.5 37.7 - - + -
256A PHE* 2.9 7.0 + - - +
257A PRO* 1.3 82.1 - - - +
259A PHE* 1.3 72.5 + - - +
260A ASP* 4.7 3.1 - - + +
312A GLN* 4.2 27.6 - - + +
313A GLY 4.3 3.6 - - - +
314A PHE* 3.4 16.8 - - - +
315A ALA* 3.0 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A PHE* 3.9 20.9 - + + +
258A LEU* 1.3 79.9 - - - +
260A ASP* 1.3 59.1 + - - +
261A ILE* 3.8 24.3 + - + -
268A VAL* 3.9 21.8 - - + -
282A PHE* 3.6 33.9 - - + -
283A HIS 3.7 18.2 - - - -
286A SER 3.7 8.5 - - - -
287A ARG* 3.4 30.8 + - - +
288A PRO* 3.4 34.1 - - + -
313A GLY 3.9 2.9 - - - -
314A PHE* 3.9 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LEU* 4.7 2.0 - - + +
259A PHE* 1.3 73.5 - - - +
261A ILE* 1.3 78.0 + - - +
262A ARG* 2.9 35.4 + - - -
311A ALA* 3.8 3.1 - - - +
312A GLN* 3.1 48.0 - - + +
313A GLY 2.7 31.7 + - - +
----------------------------------------------------------
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