Contacts of the strand formed by residues 16 - 22 (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 LEU 16 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN* 3.3 11.2 + - + +
15A PRO* 1.3 80.6 - - - +
17A LEU* 1.3 55.7 + - - +
62A ALA 3.7 0.3 - - - -
63A GLY* 2.6 39.5 + - - +
64A GLY 4.2 5.6 - - - +
98A ILE* 3.7 10.3 - - - +
121A GLY* 3.6 28.7 - - - +
122A LYS 4.0 1.6 - - - +
123A VAL* 3.6 25.6 - - + -
136A THR* 3.9 6.5 - - + -
137A TYR 4.3 0.4 - - - +
138A LEU* 3.9 22.9 - - + +
141A ALA* 4.3 5.4 - - + -
401A ADN 3.5 47.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 1.3 71.5 - - - +
18A ASP* 1.3 67.3 + - - +
19A ILE* 3.7 12.4 + - + +
60A TYR* 4.1 16.6 - - + -
61A ILE 3.9 17.5 - - - +
62A ALA* 4.3 0.9 - - - +
94A GLN* 3.7 32.1 - - + +
97A TYR* 3.7 36.1 - - + -
98A ILE* 4.0 8.4 - - + +
121A GLY 3.1 16.7 + - - +
122A LYS* 3.2 8.4 - - + +
123A VAL 2.8 25.6 + - - -
93B ILE* 4.0 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU 3.8 0.6 + - - +
17A LEU* 1.3 74.1 - - - +
19A ILE* 1.3 62.6 + - - +
20A ILE* 3.9 5.9 - - + +
59A ASN 3.4 4.7 - - - +
60A TYR* 3.5 3.3 - - - -
61A ILE* 2.8 50.7 + - + +
62A ALA 4.4 2.1 - - - +
63A GLY* 3.7 10.7 - - - -
123A VAL* 3.5 11.9 - - - +
125A VAL* 4.2 13.0 - - + -
298A ASN* 4.1 8.5 + - - -
338A PHE* 5.3 4.2 + - - +
401A ADN 2.4 52.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.1 15.3 - - + +
18A ASP* 1.3 76.0 - - - +
20A ILE* 1.3 62.3 + - - +
21A VAL* 3.7 4.2 + - - +
49A TYR* 5.2 6.1 - - + -
52A ILE* 3.9 22.9 - - + -
53A GLN* 4.5 13.9 - - - +
58A LEU* 4.1 18.4 - - + -
59A ASN 3.7 2.7 - - - +
60A TYR* 4.0 31.6 - - + -
122A LYS* 4.3 26.0 - - + -
123A VAL 2.8 17.4 + - - +
124A ALA* 3.8 1.7 - - - -
125A VAL 2.9 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASP* 4.3 10.3 - - + -
19A ILE* 1.3 73.9 - - - +
21A VAL* 1.3 62.7 + - - +
57A LYS 4.0 2.8 - - - +
58A LEU* 3.7 5.8 - - - -
59A ASN* 2.9 55.3 + - + +
61A ILE* 3.7 25.8 - - + -
125A VAL* 3.5 18.8 - - + +
127A VAL* 3.9 25.6 - - + -
296A ASP* 4.6 7.0 - - - +
298A ASN* 5.3 3.4 - - - +
336A SER* 5.8 0.2 - - - -
337A GLY* 3.8 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE 4.1 6.3 - - - +
20A ILE* 1.3 76.6 - - - +
22A ASP* 1.3 73.3 + - - +
23A ALA* 3.2 4.9 + - + +
52A ILE* 3.9 30.7 - - + -
55A LYS* 3.7 29.6 - - + -
56A LYS 5.2 1.6 - - - +
57A LYS 5.2 3.1 - - - -
58A LEU* 3.5 15.5 - - + -
125A VAL 3.0 12.4 + - - +
126A LEU* 3.9 14.4 - - + -
127A VAL* 2.8 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 1.3 79.8 - - - +
23A ALA* 1.3 63.9 + - - +
55A LYS* 3.9 18.7 - - + +
56A LYS 5.7 1.6 + - - +
57A LYS* 5.1 15.5 + - + +
127A VAL* 3.3 22.6 - - - +
128A SER* 5.7 0.2 - - - -
----------------------------------------------------------
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