Contacts of the strand formed by residues 116 - 121 (chain F) in PDB entry 5CEV
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 116 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F LEU* 3.7 28.3 - - + -
109F VAL* 3.8 15.5 - - + -
110F ALA* 3.6 31.0 - - + +
113F TYR* 3.9 31.4 + - + +
114F GLU 4.0 1.2 - - - -
115F ARG* 1.3 74.5 - - - +
117F GLY* 1.3 68.5 + - - +
163F LYS 4.9 1.9 + - - +
164F ILE* 3.7 25.3 - - + +
168F HIS* 3.6 14.9 + - - +
218F THR* 4.2 0.7 - - - -
219F ASP* 3.7 0.4 + - - -
220F GLY* 3.6 25.1 - - - -
221F VAL 3.9 2.0 - - - +
222F HIS* 4.1 8.3 - - + +
265F THR* 4.3 3.4 - - - +
266F SER* 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F ARG 3.6 1.6 + - - -
116F LEU* 1.3 75.3 - - - +
118F VAL* 1.3 69.6 + - - +
168F HIS 3.2 11.7 - - - -
214F LEU* 4.5 1.8 - - - -
218F THR* 3.6 15.5 - - - +
220F GLY 2.8 14.5 + - - -
221F VAL* 4.0 8.7 - - - -
222F HIS 2.8 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F LEU* 4.0 17.0 - - + -
116F LEU* 4.8 0.2 - - + -
117F GLY* 1.3 82.1 - - - +
119F ILE* 1.3 70.1 + - - +
120F TRP* 3.8 33.7 - - + +
143F LEU* 4.9 3.1 - - + -
164F ILE* 3.7 35.9 - - + -
168F HIS 2.9 7.4 + - - +
169F VAL* 3.4 14.9 - - + +
170F VAL* 3.0 26.3 + - - +
214F LEU* 4.3 2.4 - - - +
221F VAL* 4.4 0.6 - - - +
222F HIS* 3.3 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F VAL* 1.3 71.9 - - - +
120F TRP* 1.3 61.2 + - - +
121F TYR* 3.7 9.3 + - + +
170F VAL* 3.4 5.4 - - + +
172F ILE* 3.9 26.2 - - + -
207F MET* 5.0 1.8 - - + -
210F THR* 3.8 19.5 - - + -
214F LEU* 3.5 24.5 - - + -
221F VAL* 3.9 13.0 - - + -
222F HIS 3.0 7.7 + - - +
223F LEU* 3.8 19.1 - - + +
224F SER* 2.9 29.5 + - - +
258F LEU* 3.7 33.0 - - + -
263F ILE* 4.8 2.7 - - + -
264F ILE* 4.3 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F HIS* 3.2 22.2 - + - -
102F ALA* 3.5 28.3 - - + -
106F LEU* 4.4 13.0 - - + -
118F VAL* 3.8 15.9 - - + -
119F ILE* 1.3 73.1 - - - +
121F TYR* 1.3 61.2 + - - +
122F ASP* 3.1 26.4 + - + -
124F HIS 3.9 2.0 - - - -
125F GLY 4.0 0.6 + - - -
126F ASP* 3.0 35.2 + - + +
142F PRO* 3.7 15.7 - - + -
143F LEU* 3.9 32.5 - - + -
169F VAL* 5.0 1.3 - - + -
170F VAL 2.8 10.6 + - - +
171F LEU* 3.4 35.7 - - + +
172F ILE 2.9 23.9 + - - +
224F SER* 3.6 26.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F ILE* 3.7 5.9 + - + -
120F TRP* 1.3 68.8 - - - +
122F ASP* 1.3 61.7 + - - +
172F ILE* 3.5 30.5 - - + +
203F MET* 3.7 8.8 - - + +
207F MET* 5.2 2.2 - - - -
223F LEU* 4.6 7.2 - - + -
224F SER 3.2 9.4 + - - +
225F LEU* 3.7 37.0 - - + -
226F ASP* 2.9 32.7 + - - +
229F GLY* 4.8 2.5 - - - -
230F LEU* 4.1 12.3 - - + -
246F LEU* 3.3 30.3 - - + +
251F SER* 2.9 41.6 + - - -
254F ALA* 4.0 19.9 - - + +
255F MET* 4.5 6.5 - - + -
258F LEU* 6.4 0.2 - - + -
----------------------------------------------------------
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