Contacts of the helix formed by residues 138 - 143 (chain A) in PDB entry 1VHA
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 138 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A THR* 2.7 41.2 + - - +
136A GLU 3.7 7.9 - - - +
137A LYS* 1.3 83.9 - - + +
139A GLY* 1.3 63.3 + - - +
141A THR* 4.0 0.7 + - - -
142A GLY 2.9 8.1 + - - -
170A ACY 4.0 0.2 + - - -
10C VAL* 4.2 3.1 - - + -
12C ALA* 3.7 22.4 - - + -
140C PHE* 3.6 37.2 - - + -
145C GLU* 3.6 45.3 - - + +
146C GLY* 4.0 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LYS 4.3 0.2 + - - -
138A LEU* 1.3 73.1 - - - +
140A PHE* 1.3 60.9 + - - -
141A THR 3.2 0.9 - - - -
143A ARG* 2.8 41.2 + - - +
170A ACY 3.8 3.6 - - - -
170B POP 3.3 24.7 + - - -
140C PHE* 3.6 17.5 - - - +
145C GLU* 4.9 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 5.2 1.8 - + - -
10A VAL* 3.8 42.0 - - + -
139A GLY* 1.3 72.1 - - - -
141A THR* 1.3 82.6 + - + +
143A ARG* 3.6 7.7 + - - +
144A GLN 3.3 2.9 + - - -
145A GLU* 2.9 52.8 + - + +
146A GLY 4.6 2.5 - - - -
147A ILE 4.5 2.2 - - - -
148A ALA* 4.4 3.6 - - + -
170A ACY 3.6 20.1 + - + -
135B THR* 4.7 2.9 - - + -
138B LEU* 3.8 24.5 - - + -
139B GLY* 3.7 23.1 - - - +
170B POP 3.2 23.6 + - - +
171B ACY 4.1 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ILE* 3.6 29.7 - - + +
101A ALA* 4.7 4.7 - - - -
102A GLN* 3.2 19.6 + - - +
135A THR* 3.0 20.4 + - - +
140A PHE* 1.3 102.0 - - + +
142A GLY* 1.3 60.9 + - - +
144A GLN* 3.0 16.5 + - - -
146A GLY 3.6 17.6 - - - +
148A ALA* 3.9 11.4 - - + +
170A ACY 2.8 19.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLN* 3.4 29.0 - - - +
135A THR* 3.5 1.6 - - - -
137A LYS* 3.5 27.0 - - - +
138A LEU 2.9 24.4 + - - -
141A THR* 1.3 82.2 + - - +
143A ARG* 1.3 55.0 + - - +
144A GLN* 3.3 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LYS 4.7 8.1 - - - +
139A GLY* 2.8 24.1 + - - +
140A PHE* 3.6 5.8 - - - +
141A THR 3.3 0.2 - - - -
142A GLY* 1.3 74.6 - - - +
144A GLN* 1.3 71.7 + - - +
145A GLU* 2.9 48.9 + - + +
139B GLY 5.2 0.4 - - - +
143B ARG* 4.3 5.5 - - - +
170B POP 2.3 46.1 + - - -
143C ARG* 4.2 5.7 - - - +
----------------------------------------------------------
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