Contacts of the helix formed by residues 154 - 163 (chain A) in PDB entry 3VON
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 154 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 4.5 0.9 - - - -
153A THR* 1.3 79.6 + - - +
155A VAL* 1.3 62.4 + - - +
156A ALA* 3.1 16.9 + - - +
157A ASP* 3.1 25.1 + - - +
158A LEU* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 5.8 1.8 - - - -
83A ARG* 4.1 11.4 - - - +
98A PHE* 4.0 11.2 - - + -
102A GLU* 3.5 37.7 - - + +
105A LEU* 4.4 16.4 - - + -
153A THR 3.9 0.2 + - - -
154A SER* 1.3 74.5 + - - +
156A ALA* 1.3 57.0 + - - +
158A LEU* 3.5 7.0 + - + +
159A LEU* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU* 6.1 0.4 - - - +
83A ARG* 6.2 0.2 - - - +
154A SER* 3.1 10.5 + - - +
155A VAL* 1.3 77.4 - - - +
157A ASP* 1.3 68.1 + - - +
159A LEU* 3.6 12.3 + - + +
160A ALA* 3.3 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLN* 3.6 12.0 + - - +
153A THR* 3.2 21.7 + - - +
154A SER* 3.1 28.2 + - - +
156A ALA* 1.3 78.2 - - - +
158A LEU* 1.3 63.9 + - - +
160A ALA* 3.7 7.3 + - - +
161A SER* 3.7 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 3.7 25.1 - - + -
101A LEU* 4.2 13.2 - - + +
102A GLU* 4.0 30.5 - - + +
105A LEU* 4.7 6.3 - - + -
145A LEU* 4.9 6.7 - - + +
148A GLN* 4.0 17.0 - - - +
149A VAL* 3.8 23.8 - - + -
153A THR* 4.0 15.0 - - + -
154A SER 3.0 15.7 + - - +
155A VAL* 3.7 5.6 - - - +
157A ASP* 1.3 75.4 - - - +
159A LEU* 1.3 63.5 + - - +
161A SER* 3.2 13.7 + - - -
162A PHE* 3.2 22.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 3.9 10.3 - - + +
49A SER 3.3 26.7 - - - +
50A GLU* 3.5 25.1 - - - +
83A ARG* 3.4 20.4 - - - +
98A PHE* 3.8 13.4 - - + -
155A VAL 3.0 17.8 + - - +
156A ALA* 3.8 12.6 - - + +
157A ASP 3.4 0.2 - - - -
158A LEU* 1.3 77.8 - - - +
160A ALA* 1.3 64.6 + - + +
162A PHE* 3.2 4.0 + - - +
163A ASN* 3.0 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ALA 3.3 15.3 + - - +
157A ASP* 4.0 7.4 - - - +
158A LEU 3.3 1.0 - - - -
159A LEU* 1.3 82.9 - - + +
161A SER* 1.3 59.2 + - - +
163A ASN* 3.9 6.8 + - - +
164A ASP* 3.8 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 3.9 8.4 - - - +
148A GLN* 3.8 22.4 + - - -
157A ASP 3.7 8.3 + - - -
158A LEU 3.2 9.8 + - - -
159A LEU 3.2 0.6 - - - -
160A ALA* 1.3 77.2 - - - +
162A PHE* 1.3 63.7 + - - +
163A ASN 3.3 0.7 - - - -
164A ASP* 3.6 10.1 - - - +
167A THR* 3.5 40.2 + - - +
168A SER* 4.2 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 3.8 10.2 - - - +
48A VAL* 3.9 26.5 - - + +
94A ARG* 3.7 12.3 - - + -
97A GLY 3.4 24.7 - - - -
98A PHE* 3.7 33.7 - + + -
101A LEU* 4.1 13.2 - - + -
145A LEU* 3.9 22.9 - - + -
158A LEU* 3.2 25.0 + - + +
159A LEU* 3.2 10.2 + - - +
161A SER* 1.3 78.9 - - - +
163A ASN* 1.3 59.2 + - - +
164A ASP 3.3 2.7 - - - -
168A SER* 3.0 40.3 + - - +
171A LEU* 4.0 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PRO* 3.7 6.6 - - - +
47A LEU* 2.8 52.5 + - + +
48A VAL* 3.0 31.2 + - - +
159A LEU* 3.0 39.7 + - - +
160A ALA* 3.9 6.7 + - - +
161A SER 3.3 0.4 - - - -
162A PHE* 1.3 74.5 - - - +
164A ASP* 1.3 61.0 + - - +
165A GLN* 3.5 2.4 + - - +
----------------------------------------------------------
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