Contacts of the helix formed by residues 113 - 124 (chain B) in PDB entry 3IH9
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 ILE 113 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS* 3.6 2.0 - - - +
92B SER* 4.0 16.6 - - - +
93B GLY 4.2 9.6 - - - +
94B GLU* 3.5 12.3 - - - +
96B PHE* 6.1 2.7 - - + -
108B PRO* 4.6 0.2 - - + -
109B ASP* 4.2 24.7 - - + +
110B ASN* 3.3 36.3 - - - +
112B MET* 1.3 81.1 - - - +
114B ASN* 1.3 65.1 + - - +
115B ALA* 4.2 18.2 - - + +
116B GLY* 3.1 8.1 + - - +
117B ALA* 2.9 18.9 + - - +
240B SER 5.5 0.4 - - - +
243B TYR* 3.9 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER* 4.3 0.9 + - - -
67B LYS* 2.7 33.2 + - - +
94B GLU* 2.6 24.6 + - - +
113B ILE* 1.3 69.0 - - - +
115B ALA* 1.3 63.7 + - - +
117B ALA* 2.9 4.8 + - - +
118B LEU* 2.8 28.6 + - - +
166B ARG* 3.7 14.8 - - - +
167B ASN* 3.1 26.0 + - - +
170B LEU* 3.6 17.5 - - + -
191B TYR* 3.3 13.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLU* 4.6 0.6 + - - -
96B PHE* 4.6 22.0 - - + -
108B PRO* 3.9 17.5 - - + +
113B ILE* 3.4 11.7 - - + +
114B ASN* 1.3 76.5 - - - +
116B GLY* 1.3 61.6 + - - +
118B LEU* 4.5 1.6 - - - -
119B ALA* 3.2 20.1 + - - +
170B LEU* 4.0 15.6 - - + +
174B LEU* 3.5 28.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B VAL* 4.1 2.7 - - - +
108B PRO* 3.7 18.4 - - - +
110B ASN 3.2 25.8 + - - -
111B ALA* 4.1 4.2 - - - -
113B ILE* 3.1 5.8 + - - +
115B ALA* 1.3 76.6 - - - +
117B ALA* 1.3 60.2 + - - +
119B ALA* 3.6 2.9 + - - +
120B VAL* 3.0 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS* 3.4 30.7 - - + -
70B THR* 5.4 2.2 + - - +
111B ALA 4.1 5.1 + - - +
113B ILE 2.9 4.0 + - - +
114B ASN 2.9 7.7 + - - +
116B GLY* 1.3 75.4 - - - +
118B LEU* 1.3 60.2 + - - +
120B VAL* 3.1 8.2 + - - +
121B HIS* 2.9 29.5 + - - +
191B TYR* 3.3 31.8 - - + -
194B GLN* 5.1 2.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
114B ASN 2.8 19.1 + - - +
115B ALA 3.7 4.3 - - - +
117B ALA* 1.3 77.2 - - - +
119B ALA* 1.3 61.4 + - - +
121B HIS* 3.3 3.5 + - - -
122B GLN* 3.2 17.8 + - - +
167B ASN* 3.6 29.8 - - + +
170B LEU* 3.7 22.9 - - + -
171B ALA* 3.9 8.1 - - - +
174B LEU* 3.9 9.4 - - + -
180B LEU* 4.2 2.5 - - + -
187B ILE* 3.5 28.4 - - + +
188B VAL* 4.1 15.5 - - + -
191B TYR* 3.5 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLN* 4.0 16.6 - - + +
87B VAL* 4.1 5.8 - - + -
108B PRO* 4.1 2.5 - - + -
115B ALA 3.2 16.7 + - - +
116B GLY 3.8 5.4 - - - +
117B ALA 3.2 0.2 - - - -
118B LEU* 1.3 75.5 - - - +
120B VAL* 1.3 64.4 + - - +
122B GLN* 3.1 17.8 + - - +
123B LEU* 3.3 13.3 + - - +
174B LEU* 4.4 0.2 - - - +
179B VAL* 3.6 28.0 - - + +
180B LEU* 3.8 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS 5.2 0.4 - - - +
70B THR* 3.6 44.6 - - - +
71B TYR* 3.7 15.7 - - + +
74B ALA* 4.0 5.6 - - + +
83B VAL* 5.0 3.6 - - + -
87B VAL* 3.7 18.4 - - + -
111B ALA* 3.9 18.6 - - + -
116B GLY 3.0 26.3 + - - +
117B ALA* 3.4 7.2 - - - +
119B ALA* 1.3 77.2 - - - +
121B HIS* 1.3 63.2 + - - +
123B LEU* 3.2 18.6 + - - +
124B LEU* 3.3 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ALA 2.9 11.9 + - - +
118B LEU* 3.7 9.2 - - - +
119B ALA 3.2 0.2 - - - -
120B VAL* 1.3 78.8 - - - +
122B GLN* 1.3 64.1 + - - +
124B LEU* 3.1 29.9 + - + +
131B ARG 5.1 1.6 - - - -
134B ARG* 3.4 44.5 + - + +
135B LEU* 4.3 6.0 - - + -
138B ALA* 4.4 3.2 - - + +
187B ILE* 4.6 15.7 + - + +
190B GLY* 3.4 38.4 + - - -
191B TYR* 3.9 9.6 + - + -
194B GLN* 2.8 30.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG* 4.7 2.0 + - - +
118B LEU 3.2 3.2 + - - +
119B ALA 3.1 11.6 + - - +
121B HIS* 1.3 78.9 - - - +
123B LEU* 1.3 58.7 + - + +
126B GLY 4.6 0.2 - - - +
127B PRO 5.1 1.0 + - - -
134B ARG* 3.0 37.3 + - - +
179B VAL 4.3 2.7 - - - +
180B LEU* 3.7 23.3 - - + -
181B GLN* 3.3 36.9 + - - +
182B ASP* 3.1 50.1 + - - +
187B ILE* 3.5 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ALA* 4.4 6.8 - - + +
78B ARG* 3.0 64.8 + - + +
82B ALA* 3.8 18.6 - - + +
83B VAL* 4.0 33.2 - - + -
86B GLN* 4.1 24.2 - - + -
87B VAL* 4.6 1.3 - - + -
119B ALA 3.3 14.8 + - - +
120B VAL* 3.2 13.6 + - - +
121B HIS 3.1 0.8 - - - -
122B GLN* 1.3 80.9 - - + +
124B LEU* 1.3 63.6 + - - +
125B VAL 3.1 2.8 + - - -
126B GLY 4.6 0.2 - - - -
181B GLN* 5.7 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B THR* 3.7 20.4 - - + +
73B ALA* 3.7 29.4 - - + -
74B ALA* 3.8 7.9 - - + +
77B ASP* 2.6 31.9 - - - +
120B VAL 3.3 8.0 + - - +
121B HIS* 3.1 34.8 + - + +
122B GLN 3.4 0.6 - - - -
123B LEU* 1.3 76.2 - - - +
125B VAL* 1.3 60.1 + - + +
134B ARG* 3.5 32.5 - - + +
137B ARG* 3.7 4.3 - - + +
138B ALA* 3.7 21.5 - - + +
----------------------------------------------------------
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