Contacts of the strand formed by residues 68 - 76 (chain B) 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 LEU 68 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU 3.3 2.0 - - - -
67B GLY* 1.3 80.0 - - - +
69B GLN* 1.3 60.8 + - - +
70B ALA 4.1 0.2 - - - -
112B ALA 3.9 0.3 - - - +
113B PHE* 3.4 6.6 - - - +
114B PHE* 2.8 46.7 + - + +
115B THR 4.2 0.2 + - - -
116B ASP* 3.5 35.2 - - - +
117B MSE 3.6 20.9 - - + +
120B PHE* 3.9 14.8 - - + -
141B PHE* 3.7 27.1 - - + -
142B VAL 5.5 0.2 - - - +
1012B CL 4.5 2.0 - - + -
117G MSE 3.8 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE* 3.7 32.8 - - - -
61B PRO* 5.7 0.2 - - - +
67B GLY 4.1 1.2 + - - -
68B LEU* 1.3 74.7 - - - +
70B ALA* 1.3 64.4 + - - +
71B PHE* 4.2 5.7 - - + -
111B GLN* 4.1 17.2 - - - +
112B ALA 3.4 7.6 - - - +
113B PHE* 3.4 41.0 - - + -
141B PHE* 3.3 6.5 - - - +
142B VAL* 2.9 57.9 + - + +
145B GLU* 4.8 4.0 - - - +
148B HIS* 6.1 1.0 - - - -
902B GOL 5.2 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 4.1 0.8 - - + -
69B GLN* 1.3 75.3 - - - +
71B PHE* 1.3 62.5 + - - +
72B ILE* 3.9 9.2 - - + -
110B LEU 3.6 0.5 - - - +
111B GLN* 3.4 6.2 - - - +
112B ALA 2.8 37.1 + - - +
114B PHE* 4.1 5.8 - - + -
120B PHE* 3.6 34.1 - - + -
139B SER* 5.0 0.2 - - - -
140B SER 3.4 5.2 - - - +
141B PHE* 3.8 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 4.9 3.1 - + - -
100A PHE* 3.6 25.6 - + - -
102A LEU* 3.7 22.9 - - + -
109A LEU* 3.6 27.8 - - + -
111A GLN* 5.4 0.4 - - - -
69B GLN* 4.2 6.3 - - - -
70B ALA* 1.3 73.9 - - - +
72B ILE* 1.3 60.2 + - - +
73B ARG* 4.0 3.8 + - + +
109B LEU* 4.2 22.9 - - + -
110B LEU 3.2 4.7 - - - +
111B GLN* 3.3 45.1 - - + -
139B SER* 3.3 3.1 - - - -
140B SER* 2.8 45.2 + - - +
142B VAL* 3.7 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ALA* 4.1 11.7 - - + +
71B PHE* 1.3 74.5 - - - +
73B ARG* 1.3 61.9 + - - +
74B VAL* 3.6 10.4 + - + -
108B TYR 3.4 4.3 - - - +
109B LEU* 3.5 1.8 - - - -
110B LEU* 2.8 56.1 + - + +
112B ALA* 4.4 16.4 - - + -
120B PHE* 3.8 19.5 - - + -
123B PHE* 4.1 23.3 - - + -
124B VAL* 5.8 0.4 - - + -
128B LEU* 3.7 25.1 - - + -
137B ALA* 4.0 8.7 - - + -
138B GLN 3.7 2.0 - - - +
139B SER* 3.3 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 3.1 42.1 - - - +
102A LEU* 6.0 2.6 - - - +
105A GLU* 4.3 15.6 + - - +
106A THR* 3.6 20.6 + - - +
71B PHE* 4.9 3.3 - - + +
72B ILE* 1.3 72.0 - - - +
74B VAL* 1.3 61.3 + - - +
75B SER 4.0 0.3 + - - -
105B GLU* 4.3 7.9 + - - +
106B THR* 3.4 28.4 + - + +
108B TYR 3.5 5.4 - - - -
109B LEU* 4.0 15.0 - - + +
137B ALA* 3.3 3.0 - - - -
138B GLN* 2.8 63.1 + - + +
139B SER* 5.8 0.2 - - - -
140B SER* 4.9 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 3.9 17.9 - - + -
73B ARG* 1.3 75.8 - - - +
75B SER* 1.3 70.4 + - - +
76B ILE* 4.5 5.4 - - + +
86B PHE* 3.8 26.0 - - + -
106B THR* 4.9 0.9 - - - -
107B ASP* 3.4 10.6 + - - +
108B TYR* 2.8 41.6 + - + +
110B LEU* 3.9 19.1 - - + -
128B LEU* 4.2 13.5 - - + -
134B VAL* 4.1 13.7 - - + -
136B ASP 3.6 7.6 - - - +
137B ALA* 4.2 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ARG 4.0 0.4 + - - -
74B VAL* 1.3 74.4 - - - +
76B ILE* 1.3 52.6 + - - +
105B GLU 6.0 1.6 - - - -
107B ASP* 3.6 11.6 + - - +
134B VAL* 3.8 2.3 - - - -
135B GLN* 2.7 56.2 + - - +
136B ASP* 2.8 28.8 + - - +
136D ASP* 5.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 4.0 3.7 + - + -
75B SER* 1.3 73.4 - - - +
77B ARG* 1.3 70.8 + - - +
78B LYS* 3.6 2.1 + - - +
82B ALA* 4.1 14.8 - - + +
83B ARG* 4.1 29.8 - - + +
86B PHE* 3.5 46.4 - - + -
107B ASP* 2.9 21.9 + - + +
108B TYR* 4.0 17.7 - - + -
133B GLY 3.2 21.3 - - - +
134B VAL* 4.7 2.0 - - - -
135B GLN* 3.1 17.1 + - - -
----------------------------------------------------------
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