Contacts of the helix formed by residues 113 - 127 (chain A) in PDB entry 2V3V
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 113 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN 3.6 1.4 + - - -
112A CYS* 1.3 76.0 - - - +
114A THR* 1.3 67.3 + - - +
115A GLU* 3.1 10.5 + - - +
116A GLU* 2.9 33.9 + - + +
117A SER* 3.2 10.2 + - - -
348A ASN* 4.0 0.4 - - - +
464A TRP 5.5 0.7 - - - +
467A ARG* 3.7 45.5 - - + +
468A ASP 3.2 29.4 - - - +
469A GLY* 3.6 24.0 - - - +
470A VAL 3.8 3.1 - - - +
471A TYR* 4.0 20.9 - - + -
481A THR* 5.6 4.5 - - - +
495A VAL* 5.5 2.0 - - + -
517A ALA* 5.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 1.3 71.2 - - - +
115A GLU* 1.3 60.2 + - - +
117A SER* 3.5 2.4 + - - -
118A TYR* 3.0 27.5 + - + +
348A ASN* 2.8 29.1 + - - +
351A GLY* 3.6 19.0 - - - +
352A GLY* 4.0 7.6 - - - +
356A GLY* 6.1 0.9 - - - -
470A VAL* 3.0 22.7 + - - +
472A GLY 4.4 0.2 + - - -
478A TYR* 5.8 1.5 - - + -
521A TRP* 3.8 14.1 - - + -
524A TRP* 3.4 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 3.6 4.1 - - + +
114A THR* 1.3 77.1 + - - +
116A GLU* 1.3 60.8 + - - +
118A TYR* 3.5 0.6 + - - -
119A VAL* 3.1 35.7 + - - +
469A GLY* 3.4 10.2 - - - -
470A VAL* 2.9 30.7 + - - +
495A VAL* 4.0 9.0 - - + -
517A ALA* 3.5 31.9 - - + +
520A VAL* 3.6 21.2 - - + +
521A TRP* 4.1 17.3 - - + +
524A TRP* 6.1 0.7 - - + -
540A ARG* 2.5 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TRP* 5.4 2.5 - - + -
112A CYS* 3.5 15.6 - - + +
113A LEU* 2.9 36.4 + - + +
115A GLU* 1.3 77.0 - - - +
117A SER* 1.3 57.2 + - - +
119A VAL* 3.4 1.3 + - - -
120A ALA* 3.0 26.6 + - - +
415A CYS* 5.6 0.8 - - - -
416A GLU* 4.0 3.2 - - - +
467A ARG* 3.0 35.1 + - - +
494A THR* 3.4 35.3 + - + -
495A VAL* 3.6 27.0 + - + +
498A LEU* 3.4 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TRP* 5.2 8.4 + - - +
109A SER 3.8 10.4 + - - -
112A CYS* 3.6 22.1 + - - +
113A LEU 3.2 5.7 + - - -
114A THR 3.8 5.2 - - - -
116A GLU* 1.3 76.4 - - - +
118A TYR* 1.3 60.2 + - - +
120A ALA* 4.0 5.2 - - - +
121A ASN* 3.0 31.4 + - - +
352A GLY* 3.4 28.0 + - - -
353A VAL* 4.4 5.4 - - - +
358A ALA* 4.4 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR* 3.0 19.3 + - + +
115A GLU* 3.6 4.9 - - - +
116A GLU 3.3 0.2 - - - -
117A SER* 1.3 75.1 - - - +
119A VAL* 1.3 69.0 + - + +
121A ASN* 3.7 4.5 - - - +
122A LYS* 3.1 31.9 + - + +
352A GLY 5.0 0.4 + - - -
356A GLY* 5.6 6.5 - - - -
364A PRO* 4.8 7.0 - - + -
382A TRP* 2.7 31.9 + + - -
514A PHE* 4.2 7.9 - + - -
520A VAL* 3.6 22.9 - - + -
523A GLU* 2.5 38.1 + - - +
524A TRP* 3.7 52.5 - + + -
527A VAL* 3.5 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLU 3.1 18.7 + - - +
116A GLU* 3.9 3.6 - - - +
118A TYR* 1.3 76.5 - - + +
120A ALA* 1.3 59.0 + - - +
122A LYS* 3.3 5.1 + - - +
123A ILE* 2.9 48.3 + - + +
495A VAL* 4.7 8.7 - - + +
498A LEU* 3.9 16.2 - - + -
499A VAL* 4.2 16.2 - - + -
512A VAL* 4.4 6.5 - - + -
514A PHE* 3.7 29.2 - - + -
520A VAL* 3.8 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TRP* 3.4 49.6 - - + +
116A GLU 3.0 17.5 + - - +
117A SER 4.0 2.5 - - - +
119A VAL* 1.3 77.3 - - - +
121A ASN* 1.3 62.8 + - - +
123A ILE* 3.3 7.6 + - - -
124A PHE* 3.2 32.1 + - - +
133A VAL* 5.1 1.1 - - - -
498A LEU* 3.9 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER 3.0 20.1 + - - +
118A TYR* 3.7 6.7 - - - +
120A ALA* 1.3 75.8 - - - +
122A LYS* 1.3 57.5 + - - +
124A PHE* 3.4 1.4 + - - +
125A LYS* 2.9 71.2 + - - +
133A VAL* 3.1 26.8 - - - +
356A GLY 3.6 10.4 - - - +
357A GLY 3.3 13.8 - - - +
358A ALA* 3.4 13.3 - - + +
364A PRO* 4.1 13.5 - - - +
382A TRP* 4.4 3.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
118A TYR* 3.1 22.2 + - + +
119A VAL* 3.6 4.3 - - - +
121A ASN* 1.3 75.6 - - - +
123A ILE* 1.3 64.2 + - + +
124A PHE 3.2 1.8 - - - -
126A GLY* 2.9 19.1 + - - -
127A GLY 3.1 5.9 + - - -
382A TRP* 3.7 58.9 + - + +
510A GLN 4.6 1.8 + - - -
511A LEU* 2.6 50.1 + - + +
512A VAL* 5.7 1.8 - - + -
514A PHE* 4.0 5.5 - - + -
523A GLU* 2.8 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL* 2.9 39.8 + - + +
120A ALA* 3.3 5.4 + - - +
122A LYS* 1.3 71.2 - - - +
124A PHE* 1.3 65.7 + - + +
127A GLY* 2.9 10.4 + - - +
128A PHE* 2.8 53.3 + - + -
498A LEU* 3.4 37.0 - - + +
501A PHE* 4.2 11.4 - - + -
502A ALA* 3.6 20.6 - - + -
507A VAL* 4.3 5.8 - - + -
511A LEU* 6.3 1.1 - - - -
512A VAL* 3.7 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 3.9 15.3 - + - -
104A VAL* 3.9 10.8 - - + -
105A ALA* 3.5 39.3 - - - -
106A TRP* 3.8 24.9 - + + -
120A ALA* 3.2 16.7 + - - +
123A ILE* 1.3 90.2 - - + +
125A LYS* 1.3 61.0 + - - +
128A PHE* 3.5 24.5 + + - +
129A GLY 3.0 10.9 + - - -
130A THR* 2.9 40.2 + - + +
132A ASN 4.2 3.8 - - - -
133A VAL* 3.4 22.2 - - + -
413A ILE* 4.1 18.4 - - + -
501A PHE* 4.6 1.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ASN* 2.9 50.0 + - - +
124A PHE* 1.3 73.7 - - - +
126A GLY* 1.3 60.4 + - - +
129A GLY* 3.6 15.6 - - - -
130A THR 3.2 15.7 - - - +
131A ASN* 3.7 29.0 - - - +
133A VAL* 4.0 13.2 - - + -
357A GLY 3.0 4.8 + - - -
359A LEU 2.7 29.6 + - - -
360A SER 4.8 0.4 - - - -
362A LEU 2.8 23.6 + - - +
363A LEU* 4.2 14.4 - - + -
369A ILE* 4.5 1.6 - - + -
382A TRP* 4.6 9.2 - - + -
388A ARG 4.1 0.7 - - - +
389A ILE* 3.9 22.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LYS* 2.9 12.4 + - - -
125A LYS* 1.3 82.1 - - - +
127A GLY* 1.3 57.7 + - - +
382A TRP* 4.4 6.8 - - - -
384A LEU* 3.4 32.4 - - - +
388A ARG* 3.0 26.4 + - - -
511A LEU* 3.6 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ARG* 5.9 0.7 + - - -
122A LYS 3.1 4.2 + - - -
123A ILE 2.9 14.3 + - - -
126A GLY* 1.3 79.5 - - - +
128A PHE* 1.3 68.9 + - - +
388A ARG* 4.2 10.3 + - - -
507A VAL* 4.1 17.3 - - - +
511A LEU* 3.8 15.2 - - - +
----------------------------------------------------------
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