Contacts of the helix formed by residues 116 - 122 (chain B) in PDB entry 4EVI
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 ARG 116 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.0 54.3 + - + +
34B GLU* 5.5 0.4 - - - +
36B ASP* 3.2 12.5 + - - +
39B ASP* 4.1 7.7 + - - -
107B LEU* 3.3 25.3 + - - +
109B LYS* 3.3 43.5 - - - +
114B ASN* 2.9 20.9 + - - +
115B ALA* 1.3 76.5 - - - +
117B SER* 1.3 63.7 + - - +
119B THR* 3.1 5.2 + - - -
120B PHE* 3.0 49.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASN* 4.4 1.8 + - - -
115B ALA 3.5 0.4 - - - -
116B ARG* 1.3 75.3 - - - +
118B LEU* 1.3 60.5 + - - +
120B PHE* 3.3 4.4 + - - +
121B CYS* 2.8 31.7 + - - +
174B LEU* 3.5 35.0 - - - +
177B GLU* 2.7 38.7 + - - +
178B GLY* 3.9 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN* 5.9 0.7 - - - +
17A TRP* 3.8 27.1 - - + +
20A PHE* 3.9 10.5 - - + -
115B ALA* 3.4 14.8 + - + +
116B ARG 3.3 0.4 - - - -
117B SER* 1.3 77.8 - - - +
119B THR* 1.3 57.4 + - - +
121B CYS* 3.6 5.6 - - + +
122B SER* 2.7 37.6 + - - -
175B PHE* 5.1 2.9 - - + +
178B GLY* 3.9 26.6 - - - +
179B MET* 3.8 21.3 - - + -
182B ASP* 5.6 2.5 - - + -
268B TRP* 5.0 3.8 - - + -
401B N7I 3.7 47.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 4.7 1.0 - - - +
20A PHE* 3.1 41.3 - - + -
29B LEU* 4.3 12.9 - - + +
30B GLN* 4.6 12.6 - - + +
33B LEU* 3.5 26.0 - - + +
107B LEU* 5.5 0.9 - - - +
115B ALA* 2.8 20.8 + - - +
116B ARG 3.3 8.3 - - - -
117B SER 3.1 0.2 - - - -
118B LEU* 1.3 77.6 - - - +
120B PHE* 1.3 63.6 + - + +
122B SER* 3.2 1.9 + - - -
123B VAL* 3.0 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLN* 3.6 22.1 - - + +
33B LEU* 3.6 32.1 - - + -
34B GLU* 3.9 28.9 - - + -
116B ARG* 3.0 50.4 + - + -
117B SER* 3.8 4.7 - - - +
119B THR* 1.3 76.1 - - + +
121B CYS* 1.3 63.7 + - - +
123B VAL* 3.6 5.3 + - - +
124B HIS* 3.2 24.9 + - - +
174B LEU* 3.9 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER 2.8 18.8 + - - +
118B LEU* 3.6 7.4 - - - +
120B PHE* 1.3 77.8 - - - +
122B SER* 1.3 60.3 + - - +
124B HIS* 3.2 19.0 - - - +
127B LEU* 3.3 13.2 - - - +
171B PHE* 3.6 25.2 - - - -
174B LEU* 3.8 21.0 - - + +
175B PHE* 3.9 25.8 - - - -
401B N7I 3.8 22.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 3.3 24.8 - - - -
21A LEU* 3.9 8.5 - - - -
23A TYR* 2.7 27.9 + - - -
118B LEU 2.7 27.3 + - - -
119B THR 3.2 1.1 + - - -
121B CYS* 1.3 74.3 - - - +
123B VAL* 1.3 59.4 + - - +
124B HIS 3.3 0.7 + - - -
127B LEU* 3.8 16.4 - - - +
128B VAL* 4.2 0.2 - - - +
325B LEU* 5.8 0.2 - - - -
401B N7I 2.8 33.2 + - - -
----------------------------------------------------------
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