Contacts of the strand formed by residues 120 - 127 (chain A) in PDB entry 3VAS
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 THR 120 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PRO 4.0 8.5 - - - +
17A LEU 4.8 0.2 - - - +
88A CYS 5.6 0.2 - - - +
89A ILE* 4.4 6.5 - - + -
90A GLY 2.9 23.7 + - - +
92A ASP* 2.8 32.5 + - - +
94A GLN* 4.1 11.6 - - + +
95A GLY* 3.3 14.8 - - - +
98A ILE* 3.8 27.4 - - + -
119A MET* 1.3 75.9 - - - +
121A GLY* 1.3 77.6 + - - +
122A LYS* 3.8 7.1 + - - +
137A TYR* 5.5 1.9 - - - -
140A ALA* 3.9 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PRO 4.5 1.8 + - - -
16A LEU* 3.6 14.1 - - - +
17A LEU* 3.1 20.3 + - - +
88A CYS 5.6 0.2 + - - -
119A MET 3.3 2.6 + - - -
120A THR* 1.3 86.3 - - - +
122A LYS* 1.3 60.0 + - - +
137A TYR* 3.1 15.0 - - - -
138A LEU 3.2 20.5 + - - -
139A GLY* 4.2 2.2 - - - -
140A ALA* 3.9 2.6 - - - +
141A ALA 4.7 1.0 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
16A LEU* 4.0 0.8 - - - +
17A LEU* 3.2 16.8 - - + +
19A ILE* 4.3 20.0 - - + -
49A TYR* 3.8 46.9 + - + +
120A THR 4.6 5.8 - - - +
121A GLY* 1.3 75.9 - - - +
123A VAL* 1.3 64.6 + - - +
135A VAL 4.1 0.5 - - - +
136A THR* 3.6 1.8 - - - +
137A TYR* 2.8 58.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.6 23.1 - - + -
17A LEU 2.8 9.3 + - - -
18A ASP* 3.5 12.0 - - - +
19A ILE* 2.8 32.7 + - - +
49A TYR* 4.7 1.1 - - - -
122A LYS* 1.3 77.7 - - - +
124A ALA* 1.3 63.3 + - - +
125A VAL* 3.3 18.2 + - + +
134A MET* 3.8 26.5 - - + -
135A VAL 3.6 3.1 - - - +
136A THR* 3.6 22.2 - - - +
401A ADN 3.4 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 3.8 5.8 - - - -
48A ILE* 4.3 12.8 - - + -
49A TYR* 3.8 19.8 - - + -
52A ILE* 3.9 21.8 - - + -
123A VAL* 1.3 71.2 - - - +
125A VAL* 1.3 59.2 + - - +
126A LEU* 3.7 13.9 + - + +
133A SER 3.6 2.1 - - - +
134A MET* 3.2 6.2 - - - -
135A VAL* 2.8 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASP* 4.2 22.9 - - + +
19A ILE 2.9 12.6 + - - +
20A ILE* 3.5 13.6 - - + +
21A VAL* 3.0 27.2 + - - +
123A VAL* 3.8 25.1 - - + +
124A ALA* 1.3 73.4 - - - +
126A LEU* 1.3 61.7 + - - +
127A VAL* 3.5 16.7 + - + -
132A ARG* 5.5 5.2 - - - -
133A SER 3.7 3.4 - - - +
134A MET* 3.9 17.9 - - + -
296A ASP* 5.7 0.4 - - - +
298A ASN* 4.3 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 3.8 15.9 - - + -
23A ALA* 3.6 11.9 - - + -
27A MET* 3.9 28.5 - - + -
28A TYR* 3.0 25.2 + - + +
33A LEU* 3.7 27.1 - - + -
48A ILE* 3.8 26.2 - - + -
52A ILE* 4.2 4.3 - - + -
124A ALA* 3.9 19.1 - - + +
125A VAL* 1.3 74.3 - - - +
127A VAL* 1.3 59.3 + - - +
132A ARG* 3.2 4.2 - - - +
133A SER 2.8 34.7 + - - +
135A VAL* 5.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 3.9 27.6 - - + -
21A VAL 2.8 15.9 + - - +
22A ASP* 3.3 19.9 - - - +
23A ALA 2.8 27.8 + - - +
28A TYR* 3.5 0.9 - - - -
125A VAL* 4.2 11.9 - - + +
126A LEU* 1.3 76.0 - - - +
128A SER* 1.3 69.9 + - - +
131A LEU 4.0 1.1 - - - -
132A ARG* 4.7 10.5 - - + +
295A ILE 6.0 1.8 - - - +
296A ASP* 4.7 16.6 - - - +
----------------------------------------------------------
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