Contacts of the strand formed by residues 112 - 122 (chain A) in PDB entry 1VRR
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 112 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A TYR* 3.2 5.4 - - - -
82A VAL* 2.8 53.6 + - + +
83A THR* 5.9 0.2 - - - -
110A GLU* 3.5 33.7 - - + +
111A ALA* 1.3 78.2 - - - +
113A LYS* 1.3 64.1 + - - +
114A SER 3.5 0.9 + - - -
164B LYS* 3.6 46.4 - - + -
176B TYR* 4.4 7.9 - - + +
178B GLU* 3.8 27.8 - - + +
3D A 5.7 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR 3.8 5.8 - - - +
81A TYR* 3.8 26.0 - - + +
111A ALA 3.9 1.8 + - - -
112A LEU* 1.3 71.7 - - - +
114A SER* 1.3 61.5 + - - +
176B TYR* 4.7 2.1 + - - -
3D A 3.5 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASN* 3.7 5.2 + - - +
80A TYR* 2.9 54.9 + - - +
82A VAL* 4.6 4.3 - - - -
112A LEU 3.5 3.5 + - - -
113A LYS* 1.3 76.3 - - - +
115A TYR* 1.3 79.6 + - - +
176B TYR* 3.8 8.2 + - - -
179B GLY* 6.0 0.7 - - - -
3D A 3.9 6.3 - - - -
4D T 2.7 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 3.4 51.0 + - - +
78A THR 3.1 17.3 - - - +
79A ASN* 3.6 13.5 - - - +
80A TYR* 3.7 8.4 + - - -
113A LYS 5.9 0.2 - - - -
114A SER* 1.3 88.4 + - - +
116A ASN* 1.3 76.4 + - - +
117A GLN* 4.2 13.0 - - + -
12C T 5.0 1.6 + - - -
13C A 5.6 0.3 + - - -
3D A 3.1 43.8 + - - -
4D T 2.9 62.5 + - - +
5D A 5.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A SER 3.9 0.7 - - - +
77A ARG* 3.4 5.5 - - - +
78A THR* 3.0 39.1 + - - +
80A TYR* 2.8 30.8 + - + -
115A TYR* 1.3 80.4 + - - +
117A GLN* 1.3 61.4 + - - +
139A TYR* 3.3 22.8 + - - -
144A LYS* 4.4 15.3 - - + +
148A PHE* 5.6 4.7 - - + -
186B ARG* 2.9 26.9 + - - +
4D T 4.0 0.2 - - - -
5D A 2.8 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLU* 3.0 42.4 + - - +
76A SER 3.6 8.9 + - - -
77A ARG* 3.2 38.9 + - - +
115A TYR* 4.2 10.4 - - + -
116A ASN* 1.3 74.7 - - - +
118A THR* 1.3 67.8 + - - +
119A ASP* 3.9 15.6 + - - +
144A LYS* 2.8 32.8 + - - -
148A PHE* 5.6 0.4 - - - -
13C A 5.5 4.2 - - - +
4D T 4.2 0.6 + - - -
5D A 3.0 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLU* 3.5 0.5 - - - -
76A SER 3.1 25.1 + - - -
116A ASN* 6.0 0.2 - - - +
117A GLN* 1.3 84.4 + - - +
119A ASP* 1.3 64.6 + - - +
120A PHE 3.2 23.7 + - - +
121A VAL* 3.7 10.3 - - + +
126A ALA* 4.3 7.2 - - + -
127A ILE 4.1 7.4 - - - +
128A GLU* 3.1 25.1 + - - +
144A LYS* 3.6 7.1 - - - +
148A PHE* 3.4 30.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LYS* 4.2 19.8 + - - +
69A GLU* 5.6 1.9 - - - +
73A TRP 4.5 0.5 - - - +
74A LYS* 3.3 12.3 - - - +
75A GLU* 3.4 18.9 + - + +
117A GLN* 3.9 20.7 + - - +
118A THR* 1.3 72.7 - - - +
120A PHE* 1.3 92.3 + - + +
127A ILE 5.1 0.6 + - - -
128A GLU* 5.7 0.8 - - - -
6D G 4.7 13.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASN* 5.4 3.6 - - - -
64A PHE* 4.4 1.6 - - + -
65A LYS* 3.8 38.1 - - + -
68A LEU* 3.8 42.6 - - + -
69A GLU* 4.7 5.2 - - + -
73A TRP* 4.1 21.3 - - + -
74A LYS 3.5 1.6 - - - -
118A THR* 3.2 6.2 + - - +
119A ASP* 1.3 110.7 - - + +
121A VAL* 1.3 68.7 + - - +
126A ALA* 3.4 0.7 - - - -
127A ILE* 2.9 58.4 + - + +
129A VAL* 4.0 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLY 4.6 0.5 - - - +
73A TRP* 3.7 3.4 - - - -
74A LYS* 2.8 31.5 + - - +
76A SER* 3.8 27.4 - - - -
118A THR* 3.7 20.0 - - + +
120A PHE* 1.3 81.9 - - - +
122A LYS* 1.3 69.1 + - - +
124A ARG* 5.1 4.7 - - - +
125A VAL 3.1 17.9 - - - +
126A ALA* 4.3 7.0 - - + -
148A PHE* 4.3 6.7 - - + -
153A LYS 5.4 5.2 - - - +
154A ILE* 6.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A HIS* 5.8 1.0 - - - +
23A ILE* 3.8 15.8 - - + +
26A GLU* 2.6 31.7 + - - -
71A LYS 2.7 25.6 + - - -
72A GLY* 3.7 16.6 - - - +
73A TRP* 3.5 26.9 - - + +
121A VAL* 1.3 78.6 - - - +
123A ASP* 1.3 92.3 + - - +
124A ARG 2.9 2.5 - - - -
125A VAL* 2.7 31.6 + - - +
----------------------------------------------------------
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