Contacts of the strand formed by residues 115 - 124 (chain A) in PDB entry 1VAV
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 PRO 115 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLN* 3.6 13.0 - - - +
103A ILE 3.5 11.2 - - - +
104A HIS* 3.8 17.2 - - + +
114A ALA* 1.3 88.5 - - + +
116A LEU* 1.3 63.3 + - - +
117A VAL 4.1 1.3 - - - +
118A LYS* 3.6 43.7 - - + +
133A LEU 6.1 0.2 - - - +
135A ARG* 2.8 43.0 + - - +
143A THR* 5.0 0.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ILE* 2.7 32.6 + - + +
104A HIS* 4.3 0.6 - - - +
105A SER 4.6 0.2 - - - +
114A ALA 3.6 2.4 + - - -
115A PRO* 1.3 74.1 - - - +
117A VAL* 1.3 75.0 + - + +
133A LEU 4.4 0.4 - - - -
134A VAL* 3.4 0.2 - - - -
135A ARG* 3.1 33.4 + - - +
164A VAL* 5.7 1.3 - - + -
170A LEU* 4.3 16.2 - - + -
183A LEU* 3.8 37.5 - - + -
187A TRP* 3.4 45.8 - - + -
192A LEU* 4.3 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLN* 3.1 7.0 - - - +
103A ILE* 3.0 29.7 + - + +
115A PRO* 3.3 0.6 - - - +
116A LEU* 1.3 94.7 - - + +
118A LYS* 1.3 75.3 + - - +
119A LEU* 4.9 1.8 - - + +
132A ALA* 4.3 7.4 - - + -
133A LEU 3.2 10.1 - - - +
134A VAL* 3.9 16.2 - - + -
162A ILE* 4.8 11.4 - - + -
170A LEU* 3.5 38.6 - - + -
172A VAL* 4.1 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 3.8 24.6 - - + +
101A GLY 3.5 6.7 - - - +
102A GLN* 3.6 13.9 - - - +
115A PRO* 3.6 37.6 - - + +
117A VAL* 1.3 76.5 - - - +
119A LEU* 1.3 59.7 + - - +
120A LEU* 3.8 0.9 + - - +
131A GLN 3.5 2.8 - - - +
132A ALA* 3.5 1.6 - - - -
133A LEU* 2.9 64.6 + - + +
143A THR* 4.9 11.4 + - - +
199A TYR* 6.1 3.1 - - + -
201A GLN* 4.6 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 3.3 5.6 - - - -
100A ILE* 2.9 42.5 + - + +
101A GLY 2.8 13.3 + - - +
117A VAL* 4.3 0.9 - - + -
118A LYS* 1.3 71.1 - - - +
120A LEU* 1.3 59.9 + - - +
130A VAL* 4.1 12.6 - - + -
131A GLN 4.0 9.6 - - - +
132A ALA* 4.0 8.3 - - + -
148A LEU* 4.2 5.8 - - + -
160A TYR* 3.3 52.3 - - + -
162A ILE* 3.5 22.9 - - + -
172A VAL* 3.7 26.0 - - + -
173A SER 5.0 0.2 - - - +
174A VAL* 4.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ARG* 3.2 65.1 - - + +
98A MET 3.6 9.4 - - - +
99A ILE* 3.5 24.5 - - + -
100A ILE* 5.2 0.2 - - - -
119A LEU* 1.3 75.2 - - - +
121A TYR* 1.3 65.2 + - - +
122A GLN* 4.1 5.8 - - + -
129A ARG 3.5 1.7 - - - +
130A VAL* 3.2 6.7 - - - +
131A GLN* 2.7 52.0 + - + +
133A LEU* 4.4 17.0 - - + -
201A GLN* 4.6 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE* 3.6 45.8 - - + +
92A VAL* 4.1 9.6 - - + -
97A ARG* 3.1 5.0 - - - +
98A MET* 2.9 39.5 + - + +
100A ILE* 4.1 21.7 - - + +
119A LEU 4.2 0.6 + - - -
120A LEU* 1.3 73.2 - - - +
122A GLN* 1.3 58.9 + - - +
123A LEU* 4.0 23.8 - - + +
128A GLY* 3.5 18.4 + - - -
129A ARG 3.4 5.4 - - - -
130A VAL* 3.8 18.4 - - + +
152A ILE* 2.8 39.6 + - + -
153A PRO 4.0 4.9 + - - -
154A LEU* 3.9 15.1 - - + +
158A PHE* 4.1 3.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A THR 5.4 4.4 + - - -
96A ARG* 3.2 10.3 - - + +
97A ARG* 3.9 23.7 + - + +
120A LEU* 3.9 13.7 + - + -
121A TYR* 1.3 76.7 - - - +
123A LEU* 1.3 63.1 + - - +
124A ARG* 3.5 27.2 + - + +
127A GLN 3.9 0.2 - - - +
128A GLY* 3.2 2.6 - - - -
129A ARG* 2.8 81.6 + - + +
131A GLN* 4.4 1.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL* 3.8 24.9 - - + -
96A ARG* 2.9 60.8 + - - +
121A TYR* 4.0 21.6 - - + +
122A GLN* 1.3 72.6 - - - +
124A ARG* 1.3 59.1 + - - +
125A LEU 3.4 17.5 - - - +
126A ASP* 3.6 23.6 - - - +
127A GLN 3.7 9.2 - - - -
128A GLY* 3.8 4.0 - - - +
152A ILE 4.9 0.2 - - - +
154A LEU* 4.1 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLN* 3.5 39.0 + - + +
123A LEU* 1.3 68.8 - - - +
125A LEU* 1.3 81.7 + - + +
126A ASP 3.1 3.1 + - - -
127A GLN* 2.9 25.6 + - + +
129A ARG* 3.5 38.5 - - - +
150A ASP* 2.8 29.5 + - - -
----------------------------------------------------------
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