Contacts of the strand formed by residues 262 - 268 (chain B) in PDB entry 5FHK
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 ARG 262 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ARG* 5.7 1.0 - - - +
144B VAL* 3.6 47.2 + - + +
145B GLY* 4.5 12.8 - - - +
146B PRO* 6.1 0.4 - - - -
159B SER* 3.4 2.2 - - - -
160B VAL* 3.0 35.9 + - + +
162B ASP* 5.1 10.1 + - - -
193B PRO* 4.8 17.2 - - - +
194B LEU* 5.4 4.9 - - - +
260B ASN* 3.3 15.2 + - + +
261B PRO* 1.3 76.0 - - - +
263B ASP* 1.3 65.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B VAL* 3.5 1.6 - - - -
145B GLY* 2.7 32.1 + - - +
146B PRO* 5.8 1.2 - - + +
156B LYS* 2.7 45.3 + - + +
158B GLY 3.5 6.3 - - - +
159B SER* 3.7 9.1 - - - +
261B PRO 5.0 2.6 - - - +
262B ARG* 1.3 77.3 - - - +
264B ILE* 1.3 59.2 + - - +
265B TYR* 3.7 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PRO* 5.1 7.2 - - + -
101B LEU* 3.9 12.1 - - + -
105B MET* 3.2 36.3 - - + -
106B MET* 5.7 2.7 - - - -
142B PHE* 5.4 2.0 - - + -
143B ARG 3.4 12.6 - - - +
144B VAL* 4.1 9.2 - - + -
156B LYS* 3.4 4.7 - - - +
157B ILE* 2.7 52.7 + - + -
158B GLY* 2.7 19.9 + - - +
159B SER 4.7 4.9 - - - +
160B VAL* 3.9 28.5 - - + -
263B ASP* 1.3 79.8 - - - +
265B TYR* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ILE 3.6 0.7 - - - +
142B PHE* 3.2 7.0 - - - +
143B ARG* 2.8 37.3 + - + +
145B GLY 3.3 19.7 - - - -
146B PRO* 3.5 38.2 - - + +
154B ALA* 4.3 10.5 - - + -
155B ARG 3.5 9.6 - - - -
156B LYS* 3.6 32.4 - - + +
157B ILE* 4.4 4.7 - - - -
263B ASP* 3.7 34.5 + - + +
264B ILE* 1.3 74.5 - - - +
266B MET* 1.3 58.1 + - - +
267B LEU* 3.9 18.8 - - + -
132E GLN* 4.9 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL* 3.5 25.8 - - + -
141B ILE 3.3 3.8 - - - -
142B PHE* 3.7 15.5 - - + -
153B ILE 3.5 3.3 - - - +
154B ALA* 3.6 1.0 - - - -
155B ARG* 2.9 47.3 + - + +
157B ILE* 4.2 9.1 - - + +
265B TYR* 1.3 73.2 - - - +
267B LEU* 1.3 62.3 + - - +
268B TYR* 4.3 10.6 - - + -
282B ILE* 3.8 29.8 - - + +
285B VAL* 3.7 29.4 - - + -
286B ILE* 3.7 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL* 3.2 7.3 - - - +
141B ILE* 2.6 62.2 + - + +
143B ARG* 3.7 31.4 - - + -
146B PRO 6.0 4.0 - - - -
152B LEU* 4.4 27.1 - - + -
153B ILE 3.2 5.2 - - - +
154B ALA* 3.6 31.0 - - + -
265B TYR* 3.9 14.6 - - + -
266B MET* 1.3 78.1 - - - +
268B TYR* 1.3 64.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ASP 3.5 20.0 - - - +
140B VAL* 4.5 2.0 - - + -
152B LEU* 3.4 11.4 - - - +
153B ILE* 2.8 65.8 + - + +
155B ARG* 5.5 3.8 - - + +
266B MET* 4.3 17.5 - - + -
267B LEU* 1.3 80.3 - - - +
269B ASN* 1.3 73.1 + - - +
274B LEU* 4.4 8.3 - - + -
278B VAL* 5.3 0.9 - - + -
279B ARG* 3.7 10.2 + - - -
282B ILE* 3.6 49.2 - - + +
286B ILE* 5.6 2.9 - - + +
137E GLU* 2.4 31.5 + - - -
----------------------------------------------------------
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