Contacts of the strand formed by residues 108 - 114 (chain C) 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 TYR 108 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ILE 3.5 1.2 - - - +
74C VAL* 2.8 42.2 + - + +
76C ILE* 3.9 30.5 - - + -
83C ARG* 2.9 47.6 + - - +
86C PHE* 3.9 20.2 - + + -
87C ALA* 5.8 0.2 - - + -
99C CYS* 3.8 16.4 - - - -
100C PHE 3.2 4.7 - - - -
101C ALA* 3.9 22.0 - - + -
106C THR* 3.2 8.8 - - - +
107C ASP* 1.3 85.3 - - + +
109C LEU* 1.3 59.7 + - - +
110C LEU* 3.8 16.8 - - + -
1016C CL 3.0 11.1 - - - +
146D ILE* 3.7 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C PHE* 4.2 25.8 - - + -
72C ILE 3.8 14.8 - - - +
73C ARG* 3.8 11.4 - - + -
98C SER 3.8 0.9 - - - +
99C CYS* 3.2 4.5 + - - -
100C PHE* 2.9 36.7 + - + +
102C LEU* 3.9 27.5 - - + +
106C THR* 4.7 1.8 - - + -
108C TYR* 1.3 72.5 - - - +
110C LEU* 1.3 66.1 + - - +
71D PHE* 3.7 36.8 - - + -
109D LEU* 4.3 1.3 - - + -
903D GOL 3.7 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ALA 3.7 0.2 - - - +
71C PHE* 3.3 6.2 - - - +
72C ILE* 2.8 55.3 + - + +
74C VAL* 4.0 20.0 - - + -
86C PHE* 4.1 17.9 - - + -
90C VAL* 4.6 4.9 - - + -
93C TRP* 4.9 1.8 - - + -
96C VAL* 3.9 33.7 - - + -
98C SER 3.3 3.6 - - - +
99C CYS* 3.4 30.1 - - + -
108C TYR* 3.8 13.5 - - + -
109C LEU* 1.3 80.7 - - - +
111C GLN* 1.3 61.2 + - - +
112C ALA 4.2 0.4 - - - -
123C PHE* 5.3 0.4 - - + -
128C LEU* 4.6 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLN* 2.9 31.3 - - + +
70C ALA 3.4 9.2 - - - +
71C PHE* 3.8 30.1 - - + -
96C VAL* 3.7 2.2 - - - -
97C LEU* 2.8 33.2 + - + +
98C SER* 3.0 29.4 + - - +
109C LEU 4.3 0.2 + - - -
110C LEU* 1.3 73.4 - - - +
112C ALA* 1.3 64.0 + - - +
113C PHE* 4.1 12.2 - - + -
148C HIS* 5.4 7.3 + - - -
71D PHE* 5.8 0.3 - - - -
100D PHE* 4.6 7.5 - - - -
111D GLN* 4.4 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU 4.1 0.2 - - - +
69C GLN* 3.6 4.7 - - - +
70C ALA 2.9 32.1 + - - +
72C ILE* 4.4 13.9 - - + -
95C GLU 2.9 20.2 - - - +
96C VAL* 4.0 11.9 - - + -
97C LEU 4.4 0.4 - - - +
111C GLN* 1.3 75.9 - - - +
113C PHE* 1.3 65.7 + - - +
114C PHE* 3.4 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C PRO* 3.6 34.8 - - + -
66C LEU* 3.9 36.5 - - + +
68C LEU 3.5 3.1 - - - -
69C GLN* 3.3 51.1 - - + -
95C GLU* 2.9 21.3 + - - +
97C LEU* 3.9 17.3 - - + -
111C GLN* 4.1 10.3 - - - -
112C ALA* 1.3 76.6 - - - +
114C PHE* 1.3 72.1 + - - +
148C HIS* 6.5 1.1 - + - -
152D LEU* 3.8 22.4 - - + -
153D PRO* 3.8 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 3.3 16.7 - - - +
68C LEU* 2.9 40.2 + - + +
70C ALA* 4.2 3.8 - - + -
95C GLU* 3.7 19.5 - - + -
112C ALA* 3.4 33.9 - - + -
113C PHE* 1.3 78.2 - - - +
115C THR* 1.3 60.7 + - - +
116C ASP 4.0 15.5 - - - +
119C ALA* 4.0 8.5 - - + -
120C PHE* 3.4 43.7 - + + +
123C PHE* 3.5 44.9 - + + -
----------------------------------------------------------
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