Contacts of the strand formed by residues 107 - 112 (chain A) in PDB entry 2JNV
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 107 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ALA* 2.7 48.4 + - + +
105A GLY 3.2 2.0 + - - -
106A ASN* 1.3 103.4 - - - +
108A VAL* 1.3 66.3 + - - +
109A ARG* 5.9 1.6 - - + -
141A VAL* 4.3 0.2 - - - +
143A ALA* 3.4 13.0 - - + +
144A VAL 3.9 4.9 - - - -
145A GLU* 3.6 40.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.6 12.3 - - + -
100A LEU* 3.4 28.7 - - + -
102A GLU 3.9 3.1 - - - +
103A ILE* 4.2 18.8 - - + -
104A ALA 4.4 0.7 - - - +
105A GLY 6.0 0.2 - - - +
107A VAL* 1.3 83.5 - - - +
109A ARG* 1.3 62.0 + - - +
110A LEU* 3.4 18.6 + - + +
134A LEU* 5.0 2.9 - - + -
141A VAL* 3.8 30.3 - - + -
143A ALA 3.4 4.0 + - - -
144A VAL* 3.5 16.1 - - + +
145A GLU 2.9 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 2.9 21.6 - - - +
101A HIS* 2.9 33.6 + - + +
102A GLU* 2.8 38.5 + - - +
103A ILE* 4.5 0.4 - - - +
104A ALA* 4.8 11.4 - - + +
107A VAL* 4.4 1.5 + - + -
108A VAL* 1.3 70.2 - - - +
110A LEU* 1.3 60.4 + - - +
145A GLU* 3.3 10.0 - - + +
146A PRO 3.4 17.5 + - - +
147A VAL* 2.9 37.0 + - - +
148A THR* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 4.2 3.4 - - + -
84A LEU* 3.7 31.0 - - + -
99A ALA 3.7 2.5 - - - +
100A LEU* 3.6 29.6 - - + +
101A HIS* 5.5 0.2 - - - -
108A VAL* 3.4 21.9 + - + +
109A ARG* 1.3 77.4 - - - +
111A LYS* 1.3 60.8 + - - +
112A LEU* 3.7 20.2 + - + +
130A ILE* 4.6 14.4 - - + -
134A LEU* 4.2 20.2 - - + -
144A VAL* 4.4 18.8 - - + -
145A GLU 3.1 8.0 + - - +
146A PRO* 3.7 22.4 - - - +
147A VAL* 4.9 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP* 3.9 10.2 - - - +
98A VAL* 3.2 26.4 - - - +
99A ALA* 2.8 27.0 + - + +
101A HIS* 4.8 6.0 - - + +
109A ARG 4.4 0.2 + - - -
110A LEU* 1.3 70.1 - - - +
112A LEU* 1.3 64.6 + - - +
113A GLN* 6.3 1.6 - - + -
147A VAL* 4.2 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 5.1 2.0 - - + -
98A VAL* 3.3 31.6 - - + -
110A LEU* 3.7 23.2 + - + +
111A LYS* 1.3 79.0 - - - +
113A GLN* 1.3 57.9 + - - +
114A GLY 3.3 6.1 + - - -
123A LEU* 3.9 22.4 - - + +
126A ILE* 3.7 16.6 - - + -
127A LYS* 4.2 19.5 - - + +
130A ILE* 3.2 47.3 - - + -
144A VAL* 5.9 4.7 - - + -
----------------------------------------------------------
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