Contacts of the helix formed by residues 114 - 125 (chain B) in PDB entry 3N1Z
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 THR 114 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B MET 4.8 4.5 - - - +
113B LEU* 1.3 74.0 - - - +
115B ARG* 1.3 64.2 + - - +
116B GLU* 3.5 16.2 + - - +
117B TRP* 3.1 25.3 + - - +
118B VAL* 3.1 26.3 + - - +
245B GLU* 5.1 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B THR* 1.3 71.3 - - - +
116B GLU* 1.3 73.4 + - - +
118B VAL* 3.3 10.1 + - - +
119B GLU* 3.0 52.2 + - - +
180B TYR* 4.3 17.1 - - - -
182B ASP* 3.5 28.8 + - - -
183B VAL* 3.6 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B THR* 3.5 13.8 + - - +
115B ARG* 1.3 85.0 + - - +
117B TRP* 1.3 65.0 + - - +
119B GLU* 2.9 21.2 + - - +
120B THR* 2.9 15.7 + - - +
245B GLU* 5.8 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 3.8 25.4 - - + -
114B THR* 3.1 20.9 + - - +
116B GLU* 1.3 79.9 - - - +
118B VAL* 1.3 63.0 + - - +
120B THR* 3.1 23.1 + - + -
121B LEU* 3.0 52.0 + - + +
238B LEU* 4.3 11.7 - - + -
241B LEU* 3.5 34.1 - - + -
242B ALA* 3.3 41.5 - - + -
245B GLU* 3.3 35.2 + - + +
247B ASP* 2.9 27.2 + - + +
250B LEU* 4.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 4.2 14.1 - - + -
114B THR 3.1 18.3 + - - +
115B ARG* 3.6 14.6 - - - +
116B GLU 3.2 0.2 - - - -
117B TRP* 1.3 75.1 - - - +
119B GLU* 1.3 63.0 + - - +
121B LEU* 3.2 13.1 + - + +
122B ALA* 3.2 17.0 + - - +
176B LEU* 6.1 0.2 - - + -
180B TYR* 3.7 46.9 - - + +
183B VAL* 3.8 28.7 - - + -
185B PHE* 3.7 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ARG* 3.0 52.6 + - - +
116B GLU* 2.9 11.5 + - - +
118B VAL* 1.3 78.1 - - + +
120B THR* 1.3 64.7 + - - +
122B ALA* 3.3 8.6 + - - +
123B ARG* 3.2 22.3 + - - +
183B VAL* 5.3 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLU* 2.9 15.6 + - - +
117B TRP* 3.1 41.0 + - + -
119B GLU* 1.3 76.8 - - - +
121B LEU* 1.3 53.8 + - - +
123B ARG* 4.5 1.1 - - - -
124B PHE* 2.6 66.5 + - + +
238B LEU* 5.1 2.0 - - + -
241B LEU* 4.6 10.3 - - + -
307B LEU* 5.1 1.1 - - + -
308B PRO* 5.4 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 4.2 6.7 - - + -
117B TRP* 3.0 49.9 + - + +
118B VAL* 3.4 11.2 - - + +
120B THR* 1.3 74.4 - - - +
122B ALA* 1.3 61.4 + - - +
123B ARG 3.0 1.8 - - - -
125B TYR* 2.9 45.1 + - + -
126B THR* 3.0 14.7 + - - -
172B ARG* 5.5 1.1 - - - +
176B LEU* 3.9 31.9 - - + -
185B PHE* 4.1 9.2 - - + -
238B LEU* 5.6 0.9 - - + -
247B ASP* 3.7 8.5 - - - +
250B LEU* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL 3.2 5.2 + - - +
119B GLU* 3.3 9.1 + - - +
121B LEU* 1.3 78.6 - - - +
123B ARG* 1.3 57.6 + - + +
126B THR* 3.4 7.1 + - - -
127B PRO* 3.4 18.5 - - - +
183B VAL* 3.6 31.6 - - + +
184B GLY 6.3 0.2 - - - -
185B PHE* 3.5 17.4 - - + +
189B GLU* 4.9 3.1 - - - +
192B VAL* 4.4 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLU 3.2 15.9 + - - +
120B THR* 3.7 3.1 - - - +
121B LEU 3.0 0.2 - - - -
122B ALA* 1.3 79.3 - - - +
124B PHE* 1.3 100.9 - - + +
127B PRO* 3.3 7.8 - - - +
192B VAL* 3.7 7.0 - - + +
196B ASP* 2.5 45.6 + - - +
197B PRO* 4.7 6.7 - - - +
198B ALA* 4.3 7.9 - - - +
199B TRP* 2.8 27.4 + - - +
306B ALA* 3.8 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B THR* 2.6 40.4 + - + +
123B ARG* 1.3 106.5 - - + +
125B TYR* 1.3 59.5 - - - +
127B PRO* 4.0 1.3 - - - -
128B ALA* 4.9 0.2 - - - +
198B ALA* 4.0 12.3 - - + -
199B TRP* 3.4 14.4 - - - -
234B LEU* 4.8 1.9 - - - +
238B LEU* 3.9 16.5 - - + +
303B TYR* 2.8 57.2 + + - +
306B ALA* 3.4 37.7 - - + -
307B LEU* 3.4 25.1 - - + -
308B PRO* 5.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B THR 3.8 0.2 + - - -
121B LEU* 2.9 41.2 + - + +
123B ARG 3.8 0.2 - - - -
124B PHE* 1.3 76.4 - - - +
126B THR* 1.3 87.0 + - + +
127B PRO* 3.2 2.0 - - - -
128B ALA* 3.0 29.1 + - + +
132B PHE* 5.6 3.6 - + - -
169B THR* 3.5 37.4 + - + +
172B ARG* 3.6 25.0 - - + +
176B LEU* 4.2 9.0 - - + -
238B LEU* 4.0 13.0 - - + +
250B LEU* 3.7 31.2 - - + -
253B LEU* 3.6 21.8 - - + +
257B GLN* 5.6 3.3 + - - -
----------------------------------------------------------
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