Contacts of the strand formed by residues 111 - 117 (chain B) in PDB entry 3JVX
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 LYS 111 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A THR* 4.5 13.7 + - - +
2B ARG* 3.9 26.5 - - - +
3B VAL 3.3 1.4 + - - -
4B SER* 3.2 13.6 - - - +
5B PHE 2.9 25.6 + - - -
92B GLU* 4.9 0.6 + - - -
109B VAL* 3.4 5.0 - - - +
110B ASP* 1.3 80.7 - - - +
112B LEU* 1.3 63.0 + - - +
113B TYR* 3.3 35.3 + - + +
135B TRP* 3.8 1.3 - - - -
138B VAL* 4.7 1.6 - - - -
157B VAL* 3.5 22.4 - - + -
158B TYR 3.4 15.3 - - - +
159B GLU* 3.3 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE* 3.8 26.5 - - + -
109B VAL* 3.8 10.1 - - + -
111B LYS* 1.3 72.2 - - - +
113B TYR* 1.3 63.4 + - - +
114B ILE* 3.6 18.5 + - + -
127B PHE* 4.4 4.5 - - + -
130B MET* 3.6 40.2 - - + -
132B MET* 3.5 32.1 - - + -
135B TRP* 3.5 20.9 - - + -
156B HIS 3.6 1.0 - - - +
157B VAL* 3.2 7.0 - - - +
158B TYR* 2.8 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B SER* 3.5 26.2 - - - -
5B PHE 2.8 21.8 + - - +
6B MET* 3.6 20.0 - - + +
7B VAL* 3.1 26.7 + - - +
31B TYR* 4.0 19.1 - - + +
35B THR* 3.5 28.7 - - + +
92B GLU* 3.0 20.1 + - - -
94B PHE* 3.7 13.9 - + - -
111B LYS* 3.3 32.4 + - + -
112B LEU* 1.3 73.7 - - - +
114B ILE* 1.3 60.6 + - - +
115B THR 4.2 0.2 - - - -
156B HIS 3.5 6.1 - - - -
157B VAL* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 3.4 21.8 - - + -
9B MET* 4.4 16.8 - - + -
13B ARG* 6.1 1.1 - - - +
31B TYR* 6.4 0.7 - - - -
112B LEU* 3.6 38.8 - - + +
113B TYR* 1.3 76.7 - - - +
115B THR* 1.3 65.5 + - - +
116B LYS* 3.7 30.3 - - + -
127B PHE* 4.6 13.0 - - + -
130B MET* 5.4 0.4 - - - -
132B MET* 5.0 4.7 - - + -
154B TYR 3.8 0.5 - - - +
155B TYR* 4.8 0.2 - - - -
156B HIS* 2.7 49.3 + - + +
158B TYR* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL 2.9 8.1 + - - -
8B ALA* 3.4 9.8 - - + +
9B MET 2.9 28.4 + - - +
28B GLU* 2.6 43.3 + - + -
31B TYR* 4.5 3.1 - - - -
113B TYR 5.6 0.2 - - - -
114B ILE* 1.3 77.2 - - - +
116B LYS* 1.3 62.4 + - - +
117B ILE* 3.9 7.4 + - + -
153B TYR* 3.8 22.9 - - + -
154B TYR 3.3 11.0 - - - +
155B TYR* 3.4 17.1 - - + -
208B EKB 3.6 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B MET* 3.5 21.3 - - + +
10B ASP 5.9 1.6 - - - +
114B ILE* 3.7 25.8 - - + -
115B THR* 1.3 71.2 - - - +
117B ILE* 1.3 63.0 + - - +
118B HIS* 3.4 14.6 - - + +
153B TYR* 3.1 3.6 - - - -
154B TYR 2.8 35.5 + - - -
156B HIS* 3.7 31.7 + - + +
158B TYR* 2.9 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ALA* 4.5 6.7 - - + -
9B MET 2.8 16.9 + - - +
10B ASP* 3.4 5.8 - - - -
11B GLU* 3.3 22.5 + - - +
23B TRP* 3.3 51.6 - - + +
25B LEU* 3.9 13.7 - - + -
28B GLU* 5.8 0.2 - - + -
115B THR* 4.4 7.2 - - + +
116B LYS* 1.3 74.9 - - - +
118B HIS* 1.3 63.6 + - - +
119B HIS* 2.9 10.4 + - + -
121B PHE* 3.9 17.5 - - + -
151B TYR* 3.8 22.7 - - + -
152B THR 3.7 10.8 - - - +
153B TYR* 3.9 11.9 - - + -
----------------------------------------------------------
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