Contacts of the helix formed by residues 156 - 168 (chain A) in PDB entry 2J25
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 156 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASP* 4.6 9.6 - - + +
90A ALA* 3.7 15.7 - - + +
91A LEU* 4.5 26.9 - - + -
94A LEU* 3.7 28.4 - - + +
151A GLU 3.3 3.8 + - - +
152A GLU* 3.1 33.2 - - + +
155A LYS* 1.3 85.2 - - + +
157A LYS* 1.3 69.3 + - + +
158A ILE 3.5 0.4 - - - -
159A PRO* 3.3 8.7 - - - +
160A LEU* 3.3 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A MET* 3.7 39.9 - - + +
86A THR 4.6 0.4 - - - +
87A ASP* 3.4 26.7 + - - +
90A ALA* 4.1 12.3 - - + -
121A VAL* 3.7 10.3 - - - -
122A PRO* 2.8 29.6 + - - +
124A ALA 4.5 5.7 + - - +
133A TYR* 4.8 1.0 + - - -
135A TYR* 3.8 2.6 + - - -
152A GLU 2.8 21.3 + - - +
153A ASP* 3.1 23.4 + - - +
156A LEU* 1.3 73.1 - - + +
158A ILE* 1.3 60.5 + - - +
160A LEU* 3.2 4.3 + - - +
161A ILE* 2.8 36.1 + - + +
220A TYR* 3.6 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LEU* 3.7 17.7 - - + -
153A ASP 2.7 27.3 + - - +
154A THR* 4.6 2.5 - - - +
157A LYS* 1.3 72.1 - - - +
159A PRO* 1.3 66.7 - - + +
161A ILE* 3.2 6.7 + - - +
162A HIS* 2.9 52.3 + - + +
220A TYR* 3.3 38.1 - - + -
223A HIS* 3.6 46.4 - - + +
225A LEU* 4.0 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 5.4 2.7 - - + -
153A ASP 3.5 2.7 - - - +
154A THR 3.2 28.3 - - - +
155A LYS* 3.2 20.9 - - - +
156A LEU 3.3 11.0 - - - +
158A ILE* 1.3 93.2 - - + +
160A LEU* 1.3 61.8 + - + +
162A HIS* 3.3 11.3 - - + +
163A ARG* 3.0 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A MET* 3.5 23.2 - - + +
90A ALA* 3.5 41.5 - - + +
93A ILE* 3.7 27.8 - - + -
94A LEU* 4.0 14.1 - - + -
105A LEU* 4.2 14.6 - - + +
156A LEU 3.3 15.4 + - - +
157A LYS 3.2 4.2 + - - +
159A PRO* 1.3 75.6 - - - +
161A ILE* 1.3 56.8 + - - +
163A ARG* 2.9 29.4 + - - +
164A ALA* 2.7 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A MET* 4.2 19.7 - - + -
119A ILE* 4.3 9.9 - - + -
121A VAL* 3.6 34.3 - - + -
157A LYS* 2.8 30.0 + - + +
158A ILE 3.7 4.0 - - - +
160A LEU* 1.3 71.9 - - - +
162A HIS* 1.3 65.4 + - - +
164A ALA* 3.1 13.3 + - - +
165A LEU* 3.1 16.6 + - + +
174A LEU* 3.9 33.7 - - + -
220A TYR* 4.3 19.7 - - + -
225A LEU* 4.1 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ILE* 2.9 39.2 + - + +
159A PRO* 3.3 11.5 - - + +
161A ILE* 1.3 75.4 - - - +
163A ARG* 1.3 65.4 + - + +
165A LEU* 3.1 9.7 + - + +
166A GLN* 3.0 25.7 + - - +
223A HIS* 2.9 31.8 + - + -
224A LYS* 3.9 10.0 + - + +
225A LEU* 3.8 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 4.0 7.1 - - - +
98A PRO* 4.5 2.0 + - - +
101A GLN* 2.9 44.1 + - - +
102A ASN* 3.2 29.4 + - - +
105A LEU* 3.8 21.8 - - + +
159A PRO* 3.0 22.4 + - - +
160A LEU* 2.9 24.3 + - - +
162A HIS* 1.3 77.1 - - + +
164A ALA* 1.3 63.2 + - - +
166A GLN* 3.3 18.5 + - - +
167A LEU* 3.0 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A MET* 5.3 1.6 - - + -
105A LEU* 4.4 7.3 - - + +
109A PHE* 3.7 39.7 - - + +
119A ILE* 3.9 17.9 - - + -
160A LEU 2.7 16.8 + - - +
161A ILE* 3.3 10.3 - - - +
163A ARG* 1.3 72.0 - - - +
165A LEU* 1.3 58.9 + - - +
167A LEU* 3.1 8.0 + - - +
168A ALA* 3.0 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE* 4.4 9.2 - - + -
161A ILE* 3.4 20.6 - - + +
162A HIS* 3.1 7.7 + - + +
164A ALA* 1.3 75.5 - - - +
166A GLN* 1.3 67.6 + - - +
167A LEU 3.0 1.3 - - - -
168A ALA* 3.0 24.6 + - - +
170A ARG 5.3 0.2 - - - +
172A VAL* 3.4 44.9 - - + +
174A LEU* 4.6 7.6 - - + -
225A LEU* 4.4 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A HIS* 3.0 12.6 + - - +
163A ARG* 3.4 30.0 + - - +
165A LEU* 1.3 76.8 - - - +
167A LEU* 1.3 70.0 + - + +
168A ALA 3.6 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ASN* 4.5 16.2 - - + +
105A LEU* 4.7 9.4 - - + +
106A LYS* 3.1 53.6 - - + +
109A PHE* 4.7 7.2 - - + -
110A SER* 3.5 21.4 - - - -
111A GLU 4.7 0.3 + - - -
163A ARG* 3.0 24.7 + - + +
164A ALA* 3.5 6.3 - - - +
165A LEU 3.0 1.0 - - - -
166A GLN* 1.3 91.1 - - + +
168A ALA* 1.3 62.9 + - - +
169A GLN* 3.7 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PHE* 3.2 19.5 - - + +
116A TYR 4.7 2.0 - - - +
164A ALA 3.0 14.3 + - - +
165A LEU 3.0 13.4 + - - +
166A GLN 4.3 2.6 - - - +
167A LEU* 1.3 79.0 - - - +
169A GLN* 1.3 62.1 + - - +
170A ARG 3.6 18.0 - - - +
172A VAL* 3.7 20.9 - - + -
----------------------------------------------------------
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