Contacts of the strand formed by residues 93 - 101 (chain A) in PDB entry 3VOR
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 GLY 93 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TYR* 3.4 21.3 - - - +
81A GLY 3.8 0.2 - - - -
82A ALA* 2.9 34.4 + - - +
84A THR* 4.3 1.8 - - - +
91A ASN* 3.6 4.7 - - - +
92A LYS* 1.3 76.6 - - - +
94A PHE* 1.3 58.5 + - - -
140A MET* 4.4 4.0 - - - -
181A SER 3.1 17.5 - - - -
182A ARG* 4.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 5.5 0.9 - - + -
18A ARG* 4.0 20.0 - - + -
21A MET* 3.7 48.0 - - + -
22A LYS* 4.7 6.7 - - + -
31A TYR* 3.6 37.0 - + + -
79A ILE* 4.7 3.8 - - + -
80A GLY 3.4 10.8 - - - +
82A ALA* 3.9 3.6 - - - +
93A GLY* 1.3 73.9 - - - +
95A ALA* 1.3 69.5 + - - +
96A MET* 5.0 7.6 - - + -
117A TRP* 3.9 32.5 - + - -
180A ALA* 3.1 3.8 - - - +
181A SER* 2.9 49.4 + - - -
182A ARG* 4.4 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ILE* 3.2 6.1 - - - +
80A GLY 2.8 32.9 + - - +
81A GLY 4.1 5.8 - - - +
82A ALA* 4.4 0.4 - - + -
94A PHE* 1.3 79.2 - - - +
96A MET* 1.3 60.9 + - - +
133A LEU* 3.9 10.7 - - + +
138A VAL* 3.6 33.2 - - + -
178A THR* 4.1 4.5 - - + -
179A LEU 3.2 9.0 - - - +
180A ALA* 3.9 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A THR* 3.6 42.6 - - + +
17A ILE* 3.8 31.9 - - + -
77A ILE* 3.6 28.0 - - + -
78A GLY 3.3 5.4 - - - +
79A ILE* 4.4 5.4 - - + +
94A PHE* 5.0 7.2 - - + -
95A ALA* 1.3 74.7 - - - +
97A GLU* 1.3 61.5 + - - +
98A LEU* 4.1 10.2 - - + +
117A TRP* 3.7 23.6 - - + -
133A LEU* 4.8 0.2 - - - -
177A ILE 3.7 1.0 - - - +
178A THR* 3.3 4.3 - - - -
179A LEU* 2.8 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASN* 5.2 0.2 + - - -
77A ILE* 4.0 2.8 - - - +
78A GLY 2.9 16.3 + - - +
96A MET* 1.3 73.1 - - - +
98A LEU* 1.3 73.1 + - - +
99A ASN 3.9 0.2 - - - -
125A SER* 2.7 30.1 + - - +
130A TYR* 3.3 45.8 + - + +
132A ALA* 3.1 23.2 + - - +
133A LEU* 3.1 37.9 + - + +
176A SER* 4.0 7.6 + - - -
177A ILE 3.3 5.2 - - - +
178A THR* 3.7 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.1 26.7 - - + -
14A THR* 4.0 31.6 - - + -
70A ASN* 4.0 8.7 - - - +
77A ILE* 4.5 8.1 - - + -
96A MET* 4.1 14.4 - - + +
97A GLU* 1.3 79.2 - - - +
99A ASN* 1.3 61.0 + - - +
101A LEU* 3.6 13.8 - - + +
109A ILE* 4.0 25.6 - - + -
176A SER* 3.1 7.1 - - - -
177A ILE* 2.8 47.6 + - + +
179A LEU* 4.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASN* 3.2 16.4 + - - +
73A SER* 2.8 29.7 + - - -
75A ASP* 2.8 24.5 + - - -
97A GLU* 3.9 0.8 - - + -
98A LEU* 1.3 73.7 - - - +
100A GLY* 1.3 65.8 + - - +
101A LEU* 3.4 9.8 + - - +
125A SER* 3.5 18.2 - - - +
126A PRO 3.3 7.8 + - - +
128A GLY 3.7 2.0 - - - +
129A SER 3.0 26.8 + - - +
130A TYR* 3.4 24.8 + - + -
175A ASN 4.0 0.2 - - - -
176A SER* 4.0 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 3.4 18.4 - - - +
99A ASN* 1.3 74.1 - - - +
101A LEU* 1.3 61.2 + - - +
102A SER 3.9 1.2 + - - -
105A GLN* 4.1 0.7 - - - +
125A SER 3.0 15.5 + - - -
126A PRO* 4.1 2.5 - - - -
127A SER* 3.3 32.3 + - - +
174A VAL* 4.6 6.3 - - - -
175A ASN 3.5 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.4 7.9 - - + -
72A ILE* 4.1 19.7 - - + -
98A LEU* 3.6 20.6 - - + +
99A ASN 3.4 17.9 - - - +
100A GLY* 1.3 74.5 - - - +
102A SER* 1.3 69.8 + - - +
105A GLN* 3.8 2.9 - - + -
106A CYS* 4.0 12.6 - - + +
109A ILE* 3.9 24.5 - - + -
173A THR 4.8 0.7 - - - -
174A VAL* 3.8 3.2 - - - -
175A ASN* 2.8 46.0 + - - +
176A SER* 4.1 2.0 - - - -
177A ILE* 3.7 35.4 - - + +
----------------------------------------------------------
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