Contacts of the strand formed by residues 124 - 129 (chain A) in PDB entry 3VTW
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 124 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 4.7 1.6 - - + -
47A PRO 3.2 15.4 + - - +
48A VAL* 3.2 20.0 - - + +
49A ILE 2.8 25.3 + - - -
98A VAL* 3.9 23.1 - - + -
110A ILE* 4.4 10.3 - - + -
113A VAL* 4.2 19.3 - - + +
114A TYR* 4.0 22.6 - - + -
117A GLU* 3.8 29.8 - - + +
118A LYS* 4.1 4.0 - - - +
122A GLY 4.1 0.2 + - - -
123A PHE* 1.3 71.6 - - - +
125A TYR* 1.3 61.9 + - - +
126A MET* 3.7 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 3.3 25.2 - + + -
23A LYS* 3.7 22.9 - - + +
31A ARG* 3.4 6.8 - - - -
49A ILE* 3.5 37.9 - - + -
51A GLU* 4.6 7.0 - - - -
97A LEU 3.8 2.8 - - - +
98A VAL* 3.8 15.1 - - - +
99A ASN* 4.6 1.6 + - - +
117A GLU 5.2 1.0 + - - -
119A ASP* 3.5 28.1 + - + +
121A ASP* 2.6 34.5 + - - -
123A PHE* 3.4 21.8 + - + +
124A LEU* 1.3 73.5 - - - +
126A MET* 1.3 69.9 + - - +
90B ALA* 3.6 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 3.6 20.9 - - + -
49A ILE 2.8 11.8 + - - +
50A ILE* 4.2 10.8 - - + -
51A GLU* 2.9 26.7 + - - +
75A MET* 4.4 13.0 - - + -
78A LEU* 3.8 25.1 - - + -
96A LEU* 4.0 29.6 - - + -
97A LEU 3.1 7.9 - - - +
98A VAL* 3.9 18.4 - - + -
110A ILE* 4.7 0.7 - - + -
124A LEU* 3.7 27.1 - - + +
125A TYR* 1.3 83.0 - - - +
127A VAL* 1.3 67.8 + - - +
90B ALA* 3.8 1.1 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
51A GLU* 3.1 20.6 - - + +
52A ARG 5.1 2.2 - - - +
53A TYR* 3.8 26.7 - - + +
96A LEU* 3.6 3.3 - - - -
97A LEU* 2.8 38.3 + - + +
126A MET* 1.3 80.9 - - - +
128A TYR* 1.3 61.3 + - - +
129A ALA* 5.2 0.4 - - + -
89B ASN* 4.6 5.2 - - + -
90B ALA* 3.9 14.3 - - + +
91B ASN* 3.4 47.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 3.8 14.4 - - + -
51A GLU 2.9 34.9 + - - -
52A ARG* 3.3 25.5 - - + +
53A TYR 3.2 22.9 + - - -
59A LEU* 3.9 14.1 - - + -
60A PRO 2.8 28.3 + - - -
62A LEU* 3.1 40.0 + - + +
82A ILE* 4.7 2.9 - - + -
86A LEU* 3.7 14.8 - - + +
94A PHE* 3.4 35.7 - + + -
95A PHE 3.1 7.4 - - - +
96A LEU* 3.9 5.8 - - + -
127A VAL* 1.3 74.6 - - - +
129A ALA* 1.3 62.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 3.8 14.6 - - + -
56A GLU* 3.3 14.8 - - - +
59A LEU* 3.3 9.7 - - - +
94A PHE* 3.4 3.8 - - - -
95A PHE* 2.8 33.7 + - - +
97A LEU* 4.9 3.5 - - + +
127A VAL* 5.2 0.2 - - + -
128A TYR* 1.3 77.5 - - - +
130A SER* 1.3 60.7 + - - +
131A GLN* 3.2 20.8 + - + +
134A PHE* 4.2 15.0 - - + -
----------------------------------------------------------
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