Contacts of the strand formed by residues 96 - 102 (chain F) in PDB entry 2P5V
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 VAL 96 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E LYS* 2.8 31.9 + - + -
149E THR* 4.7 0.9 - - - +
90F VAL* 3.9 24.9 - - + +
93F TRP* 3.0 21.2 + - + +
94F PRO 4.1 2.6 - - - +
95F GLU* 1.3 76.5 - - - +
97F LEU* 1.3 59.2 + - - +
98F SER 3.6 23.1 - - - +
110F LEU* 4.1 21.8 - - + -
111F GLN 3.6 5.8 - - - +
112F ALA* 3.9 9.6 - - + -
123F PHE* 3.8 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E LYS* 3.8 3.1 - - - +
148E HIS* 3.4 3.3 + - - -
149E THR* 2.7 53.7 + - + +
150E THR* 3.8 14.8 - - - +
151E SER 3.3 28.0 - - - +
152E LEU* 3.9 16.2 - - + -
153E PRO* 3.9 11.9 - - + -
94F PRO 3.8 10.5 - - - +
95F GLU 3.5 16.4 - - - +
96F VAL* 1.3 73.7 - - - +
98F SER* 1.3 59.8 + - - +
111F GLN* 2.9 13.8 + - + +
113F PHE* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E GLN* 5.4 1.6 + - - -
147E LYS* 3.1 15.5 - - - -
148E HIS* 3.4 23.2 + - - -
96F VAL* 3.6 6.2 - - - +
97F LEU* 1.3 83.7 - - - +
99F CYS* 1.3 62.8 + - - +
100F PHE* 3.7 16.5 - - - -
109F LEU 4.3 1.1 - - - -
110F LEU* 3.3 3.3 - - - -
111F GLN* 2.9 47.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 99 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E ILE* 2.9 39.2 + - + -
147E LYS* 2.9 12.3 + - + +
86F PHE* 4.2 6.7 - - - -
90F VAL* 3.7 27.6 - - + -
98F SER* 1.3 78.3 - - - +
100F PHE* 1.3 65.5 + - - +
108F TYR* 3.8 26.2 - - - -
109F LEU 3.3 6.1 - - - -
110F LEU* 3.9 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E GLN* 3.6 27.4 - - - -
71E PHE* 3.7 26.9 - + + -
111E GLN* 4.2 5.2 - - - -
142E VAL* 3.8 25.1 - - + -
144E LYS 3.6 2.9 - - - +
145E GLU* 3.7 28.9 - - + -
147E LYS 4.3 0.2 - - - -
148E HIS* 4.0 22.2 - + - -
98F SER* 3.7 24.0 - - - -
99F CYS* 1.3 79.4 - - - +
101F ALA* 1.3 62.2 + - - +
102F LEU* 3.6 21.8 + - + +
108F TYR* 3.2 7.5 - - - -
109F LEU* 2.9 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E VAL* 3.5 5.7 - - - -
143E LEU* 2.7 40.8 + - + -
144E LYS* 2.9 31.2 + - + +
146E ILE* 4.5 1.7 - - + +
83F ARG* 4.4 12.6 - - - +
100F PHE* 1.3 71.5 - - - +
102F LEU* 1.3 52.9 - - - +
107F ASP 3.3 10.5 - - - +
108F TYR* 3.9 22.2 - - + -
125H LEU* 5.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E PHE* 3.8 24.2 - - + -
73E ARG* 6.0 2.0 - - - +
140E SER* 4.0 19.5 - - - -
141E PHE 3.3 23.1 - - - +
142E VAL* 3.8 5.4 - - - -
143E LEU* 3.5 14.7 - - - +
100F PHE* 3.9 17.7 - - + +
101F ALA* 1.3 79.9 - - - +
103F THR* 1.3 64.6 + - - +
104F GLY 3.5 3.3 + - - +
106F THR* 3.7 26.9 - - - +
107F ASP* 3.1 11.6 + - - +
109F LEU* 3.7 34.5 - - + +
----------------------------------------------------------
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