Contacts of the helix formed by residues 123 - 140 (chain A) in PDB entry 2VGB
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 SER 123 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLY* 1.3 73.2 - - - -
124A HIS* 1.3 66.5 + - - +
125A GLU* 3.0 22.3 + - - +
126A TYR* 3.2 19.1 + - - +
127A HIS* 2.9 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 3.9 13.1 - + - -
123A SER* 1.3 71.8 - - - +
125A GLU* 1.3 78.8 + - - +
127A HIS* 3.1 4.6 + - - -
128A ALA* 2.9 20.3 + - - +
267A GLN* 3.6 13.9 + - - -
270A ARG* 3.9 22.6 + - - +
271A ASP* 2.9 35.4 + - - -
274A PHE* 3.4 40.0 - + + +
----------------------------------------------------------
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
----------------------------------------------------------
123A SER* 3.0 23.5 + - - +
124A HIS* 1.3 85.5 + - - +
126A TYR* 1.3 63.3 + - - +
128A ALA* 3.1 9.6 + - - +
129A GLU* 3.0 33.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
94A ILE 4.8 4.4 + - - -
95A GLY* 4.1 16.1 - - - -
96A PRO* 4.2 7.8 - - - +
99A ARG* 2.9 73.4 + - - +
121A HIS 4.8 1.8 - - - -
122A GLY* 4.0 13.5 - - - -
123A SER* 3.3 23.4 + - - +
124A HIS 3.1 0.6 - - - -
125A GLU* 1.3 79.9 - - - +
127A HIS* 1.3 84.2 + + - +
129A GLU* 3.6 5.6 + - - -
130A SER* 3.4 14.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.9 17.8 - - + +
118A ASN 3.6 23.1 - - - -
119A PHE* 3.5 49.3 - + + -
121A HIS 2.9 28.5 + - - -
122A GLY 3.5 8.7 + - - -
123A SER 2.9 21.7 + - - -
124A HIS 3.1 6.0 + - - +
126A TYR* 1.3 89.3 - + - +
128A ALA* 1.3 60.6 + - - +
129A GLU 3.2 0.4 - - - -
130A SER* 3.2 7.9 + - - -
131A ILE* 2.9 31.7 + - - +
274A PHE* 4.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A HIS 2.9 12.8 + - - +
125A GLU* 3.1 12.5 + - - +
127A HIS* 1.3 76.3 - - - +
129A GLU* 1.3 57.8 + - + +
131A ILE* 3.3 8.8 + - - +
132A ALA* 2.8 31.1 + - - +
274A PHE* 3.8 14.7 - - + -
278A HIS* 4.2 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 2.7 39.5 + - - +
125A GLU* 3.0 21.9 + - + +
126A TYR* 3.6 7.3 - - - +
127A HIS 3.2 0.2 - - - -
128A ALA* 1.3 76.2 - - + +
130A SER* 1.3 57.7 + - - +
132A ALA* 3.5 5.8 + - - +
133A ASN* 3.0 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ILE* 3.8 12.8 - - - +
99A ARG* 3.2 32.5 + - - +
104A LEU* 5.4 0.2 - - - +
117A LEU* 4.1 18.8 - - - -
126A TYR* 3.4 12.1 + - - -
127A HIS* 3.2 14.7 + - - -
128A ALA 3.2 0.4 - - - -
129A GLU* 1.3 76.0 - - - +
131A ILE* 1.3 66.6 + - - +
133A ASN* 3.1 4.8 + - - +
134A VAL* 3.0 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.7 26.0 - - + -
127A HIS 2.9 18.3 + - - +
128A ALA* 3.6 7.2 - - - +
130A SER* 1.3 75.8 - - - +
132A ALA* 1.3 65.3 + - - +
134A VAL* 3.1 3.0 + - - +
135A ARG* 2.9 64.5 + - - +
153A ILE* 4.2 17.7 - - + -
274A PHE* 4.0 15.0 - - + -
278A HIS* 3.8 29.4 - - + +
280A VAL* 4.4 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ALA 2.8 17.6 + - - +
129A GLU* 3.6 9.2 - - - +
131A ILE* 1.3 79.0 - - - +
133A ASN* 1.3 61.6 + - - +
135A ARG* 3.5 6.1 + - - +
136A GLU* 3.0 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 2.9 34.8 + - - +
100A SER* 4.7 1.0 - - - -
101A VAL* 3.8 26.5 + - + +
104A LEU* 4.1 5.8 - - + -
129A GLU* 3.0 26.4 + - - +
130A SER* 3.1 4.9 + - - +
132A ALA* 1.3 81.0 - - - +
134A VAL* 1.3 57.1 + - - +
136A GLU* 3.2 8.2 + - - +
137A ALA* 2.8 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ILE* 4.5 12.1 - - + -
104A LEU* 4.3 22.7 - - + -
108A ILE* 5.9 0.2 - - + -
112A MET* 5.3 3.1 - - + -
115A ALA* 4.1 20.0 - - + -
117A LEU* 5.4 2.2 - - + -
130A SER 3.0 19.9 + - - +
131A ILE* 3.5 7.0 - - - +
133A ASN* 1.3 74.4 - - - +
135A ARG* 1.3 54.9 + - - +
137A ALA* 2.8 4.8 + - - +
138A VAL* 2.7 52.9 + - + +
151A VAL* 4.1 13.0 - - + +
153A ILE* 4.0 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ILE* 2.9 41.5 + - - +
132A ALA* 3.9 5.4 - - - +
134A VAL* 1.3 75.9 - - + +
136A GLU* 1.3 56.9 + - - +
138A VAL* 3.7 6.8 - - - +
139A GLU* 2.9 44.5 + - + +
153A ILE* 3.9 20.3 - - + +
278A HIS* 2.5 34.8 + - - +
279A GLY* 3.3 19.4 + - - -
280A VAL* 4.3 1.0 - - - +
281A ASP* 5.1 1.2 + - - -
504A ARG* 5.8 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 3.6 29.7 - - + +
105A LYS* 6.1 0.2 - - - -
132A ALA 3.0 17.6 + - - +
133A ASN* 3.4 11.9 + - - +
135A ARG* 1.3 73.8 - - - +
137A ALA* 1.3 67.3 + - - +
139A GLU* 3.3 4.3 + - - +
140A SER* 3.1 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 3.9 15.6 - - + +
104A LEU* 3.4 32.5 - - + -
105A LYS* 3.9 15.3 - - + +
108A ILE* 4.0 9.2 - - + -
133A ASN 2.8 13.5 + - - +
134A VAL 3.4 7.4 - - - +
136A GLU* 1.3 71.9 - - - +
138A VAL* 1.3 60.9 + - - +
140A SER* 2.6 24.4 + - - -
141A PHE* 3.3 10.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ILE* 3.7 22.7 - - + -
134A VAL* 2.7 36.3 + - + +
135A ARG* 3.7 6.7 - - - +
137A ALA* 1.3 73.7 - - - +
139A GLU* 1.3 74.3 + - - +
140A SER 3.1 1.3 + - - -
141A PHE* 3.4 16.7 + - - +
148A TYR* 3.7 19.2 - - + +
149A ARG 3.7 23.4 - - - +
151A VAL* 3.7 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ARG* 2.9 28.0 + - + +
136A GLU* 3.8 3.6 - - - +
138A VAL* 1.3 81.4 - - - +
140A SER* 1.3 60.1 + - - +
141A PHE 3.0 6.7 + - - -
142A ALA* 3.2 26.2 + - + +
148A TYR* 3.0 31.1 + - - -
518A ARG* 4.9 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LYS* 3.5 29.2 - - - +
136A GLU* 3.1 11.8 + - - -
137A ALA 2.6 21.1 + - - -
138A VAL 3.1 0.4 - - - -
139A GLU* 1.3 78.1 - - - +
141A PHE* 1.3 69.9 + - - +
142A ALA 3.4 1.1 + - - -
143A GLY* 4.5 3.8 + - - -
----------------------------------------------------------
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