Contacts of the helix formed by residues 116 - 132 (chain A) in PDB entry 2VRB
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 PRO 116 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASN* 3.9 18.6 + - + +
114A ILE 4.0 5.1 - - - +
115A ILE* 1.4 89.3 - - + +
117A LEU* 1.3 64.1 + - - +
119A HIS* 3.0 35.3 + - + +
120A VAL* 3.7 6.1 + - - +
250A ALA* 6.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A SER* 5.3 0.4 - - - +
77A HIS 5.7 0.4 - - - +
80A ASN* 3.5 27.8 - - - +
83A LEU* 3.9 22.9 - - + -
107A TYR* 5.5 1.1 - - + -
115A ILE* 3.0 15.1 + - + -
116A PRO* 1.3 80.8 - - - +
118A ALA* 1.3 62.4 + - - +
120A VAL* 3.2 17.8 + - + -
121A HIS* 3.3 35.9 + - + +
1286A NAP 5.4 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TYR* 3.8 19.7 - - + -
110A ALA* 3.8 13.5 - - + +
113A SER* 3.4 30.5 - - - +
115A ILE* 2.8 16.0 + - - +
117A LEU* 1.3 77.7 - - - +
119A HIS* 1.3 61.3 + - + +
121A HIS* 3.3 5.6 + - - +
122A LEU* 3.0 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE* 4.5 3.9 - - + +
110A ALA 5.7 1.1 - - - -
113A SER 5.1 8.6 + - - -
114A ILE 6.5 0.4 - - - -
115A ILE 5.3 2.2 + - - -
116A PRO* 3.0 25.6 + - + +
118A ALA* 1.3 80.3 - - + +
120A VAL* 1.3 60.6 + - + +
122A LEU* 3.9 15.9 - - + +
123A ALA* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASN* 3.5 48.5 - - + +
83A LEU* 4.0 27.8 - - + -
84A ILE* 3.9 23.8 - - + +
87A HIS* 4.1 15.3 - - + +
104A TYR* 4.9 0.2 - - - +
116A PRO 4.3 3.4 - - - +
117A LEU* 3.2 13.6 + - + +
119A HIS* 1.3 78.7 - - + +
121A HIS* 1.3 55.2 + - - +
123A ALA* 3.3 2.1 + - - +
124A THR* 2.7 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A SER* 3.5 25.1 - - - -
87A HIS* 4.9 0.6 - + - -
104A TYR* 2.7 30.8 + - - -
105A THR 3.8 7.6 - - - -
106A GLY* 3.8 20.0 + - - -
107A TYR* 3.4 31.9 - + + +
110A ALA* 5.1 3.4 - - + -
117A LEU* 3.3 45.9 + - + +
118A ALA* 3.3 6.3 + - - +
120A VAL* 1.3 77.6 - - + +
122A LEU* 1.3 59.5 + - - +
124A THR* 3.3 2.6 + - - -
125A GLU* 2.9 35.9 + - - +
1286A NAP 5.0 7.7 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ALA* 3.8 30.3 - - + +
111A GLU* 3.8 22.7 - - + +
118A ALA 3.0 23.4 + - - +
119A HIS* 3.9 14.8 - - + +
121A HIS* 1.3 74.3 - - - +
123A ALA* 1.3 65.6 + - - +
125A GLU* 3.7 7.0 - - - +
126A TYR* 3.0 49.8 + - + +
139A ARG* 3.6 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE* 3.6 32.8 - - + -
119A HIS 2.9 23.2 + - - +
120A VAL 3.3 2.2 + - - +
122A LEU* 1.3 74.4 - - - +
124A THR* 1.3 58.7 + - - +
126A TYR* 3.4 6.6 + - - +
127A ALA* 2.9 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 3.7 19.7 - - + -
84A ILE* 5.5 1.4 - - - -
87A HIS* 2.9 30.1 + - + +
91A VAL* 4.5 4.0 - - + -
104A TYR* 3.4 33.7 - - + -
120A VAL* 2.7 22.7 + - - +
121A HIS 3.6 4.7 - - - -
123A ALA* 1.3 75.2 - - - +
125A GLU* 1.3 60.0 + - - +
127A ALA* 3.2 6.7 + - - +
128A ILE* 2.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A TYR* 4.2 8.7 - - + -
106A GLY* 4.7 7.4 - - - -
107A TYR 5.1 0.7 + - - -
121A HIS* 2.9 22.9 + - - +
122A LEU* 3.7 9.4 - - - +
124A THR* 1.3 74.3 - - - +
126A TYR* 1.3 60.7 + - + +
128A ILE* 3.3 2.2 + - - -
129A ARG* 2.9 40.3 + - - +
137A PHE* 3.5 48.5 - - + +
139A ARG* 2.9 53.9 + - - +
195A THR* 5.2 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLU* 5.6 2.4 + - - +
122A LEU* 3.0 48.4 + - + +
123A ALA* 3.8 6.1 - - - +
125A GLU* 1.3 80.1 - - + +
127A ALA* 1.3 59.4 + - - +
129A ARG* 3.2 29.0 + - + +
130A THR* 3.0 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS 6.0 0.2 - - - -
88A ALA* 5.3 10.8 - - + -
91A VAL* 3.6 27.9 - - + +
123A ALA 2.9 15.5 + - - +
124A THR* 3.4 10.8 - - - +
126A TYR* 1.3 74.6 - - - +
128A ILE* 1.3 60.7 + - - +
130A THR* 2.4 32.0 + - - -
131A THR 3.6 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 4.1 10.1 - - + -
91A VAL* 3.7 22.4 - - + -
102A ILE* 3.8 34.8 - - + -
104A TYR* 3.5 38.6 - - + -
124A THR* 2.9 29.9 + - + +
125A GLU 3.3 4.5 + - - +
127A ALA* 1.3 70.3 - - - +
129A ARG* 1.3 63.6 + - - +
131A THR* 2.6 26.9 + - - +
132A ASN 3.8 1.2 + - - -
133A ILE 4.5 4.1 + - - +
135A TYR* 4.0 9.1 - - + -
137A PHE* 3.8 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLU* 2.9 24.1 + - - +
126A TYR* 3.2 35.4 + - + +
128A ILE* 1.3 75.8 - - - +
130A THR* 1.3 62.3 + - + +
132A ASN* 3.4 18.3 + - - +
135A TYR* 2.8 42.2 + - + -
137A PHE* 3.7 30.7 - - + -
195A THR* 4.0 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 5.1 0.3 - - - +
126A TYR* 3.0 19.3 - - + +
127A ALA* 2.4 21.6 + - - +
129A ARG* 1.3 79.1 - - + +
131A THR* 1.3 64.8 + - - +
132A ASN* 3.4 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 3.2 35.4 - - + +
92A LYS* 5.8 0.2 - - - -
95A ARG* 3.9 31.2 - - + +
102A ILE* 5.3 0.2 - - - +
127A ALA 3.7 4.7 - - - +
128A ILE* 2.6 20.4 + - - +
130A THR* 1.3 78.5 - - - +
132A ASN* 1.3 70.7 + - - +
133A ILE* 3.1 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ILE 3.8 0.8 + - - -
129A ARG* 3.4 14.1 + - - +
130A THR 3.2 10.3 + - - +
131A THR* 1.3 80.3 + - - +
133A ILE* 1.3 64.0 + - - +
134A PRO* 3.6 6.6 - - - +
----------------------------------------------------------
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