Contacts of the helix formed by residues 107 - 119 (chain A) in PDB entry 3KQ4
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 GLY 107 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASP* 2.8 17.7 + - - -
106A PRO* 1.3 78.2 - - - +
108A ASP* 1.3 63.6 + - - -
109A LYS 3.4 0.2 - - - -
110A VAL* 3.2 18.5 + - - +
111A SER* 3.4 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASN* 3.2 23.6 + - - +
106A PRO 2.4 15.2 + - - +
107A GLY* 1.3 66.9 - - - -
109A LYS* 1.3 63.3 + - - +
111A SER* 3.4 11.6 + - - -
112A ILE* 3.2 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU 4.3 3.4 - - - -
80A MET 4.3 8.8 + - - -
82A SER* 3.4 31.4 + - - -
84A ASN* 2.7 38.2 + - - +
87A LEU* 4.6 0.8 - - + +
92A LEU* 3.9 14.3 - - + +
95A THR* 3.9 23.8 - - + -
96A ILE* 3.9 17.9 - - + +
99A LEU* 3.9 25.6 - - + -
106A PRO* 3.2 14.2 + - + +
108A ASP* 1.3 77.9 - - - +
110A VAL* 1.3 58.3 + - - +
112A ILE* 3.5 7.5 + - - +
113A LEU* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE* 3.5 32.8 - - + -
106A PRO* 3.8 17.3 - - + -
107A GLY* 3.4 14.1 - - - +
108A ASP 3.1 0.6 - - - -
109A LYS* 1.3 74.9 - - - +
111A SER* 1.3 66.1 + - - +
113A LEU* 3.3 1.2 + - - +
114A GLN* 2.9 33.2 + - - +
142A LEU* 3.9 17.5 - - + -
145A LYS* 3.8 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLY 3.4 10.1 + - - -
108A ASP* 3.5 17.7 + - - -
110A VAL* 1.3 77.3 - - - +
112A ILE* 1.3 66.0 + - - +
114A GLN* 3.1 6.3 + - - +
115A ARG* 3.0 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASN* 3.2 47.6 - - + +
85A ASN* 5.3 6.7 - - - +
92A LEU* 3.8 11.0 - - + -
108A ASP* 3.2 19.0 + - - +
109A LYS* 3.5 7.4 - - - +
111A SER* 1.3 76.3 - - - +
113A LEU* 1.3 63.0 + - - +
115A ARG* 3.3 27.6 + - - +
116A GLN* 3.0 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE* 3.9 26.9 - - + +
92A LEU* 3.7 17.7 - - + -
93A GLY* 4.0 15.5 - - - +
96A ILE* 3.8 21.3 - - + -
109A LYS 3.0 14.4 + - - +
110A VAL 3.9 3.4 - - - +
112A ILE* 1.3 79.7 - - - +
114A GLN* 1.3 57.4 + - - +
116A GLN* 3.1 3.7 + - + -
117A MET* 2.9 42.9 + - + +
138A ALA* 3.9 27.1 - - + +
141A ALA* 5.0 0.4 - - + -
142A LEU* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A VAL* 2.9 24.1 + - - +
111A SER* 3.4 7.2 - - - +
113A LEU* 1.3 77.7 - - - +
115A ARG* 1.3 61.8 + - - +
117A MET* 3.2 11.1 + - - +
118A GLU* 3.3 25.8 + - + +
142A LEU* 3.7 39.1 - - + +
145A LYS* 5.7 0.7 - - - +
146A ASN* 4.9 10.7 + - - +
149A ALA* 3.8 27.1 + - - +
150A THR* 3.9 10.6 + - - +
153A ILE* 4.6 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A SER* 3.0 23.2 + - - +
112A ILE* 3.3 40.1 + - - +
114A GLN* 1.3 75.8 - - - +
116A GLN* 1.3 68.0 + - + +
117A MET 3.3 0.5 + - - -
118A GLU* 3.5 22.1 + - - +
119A ASN* 3.9 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASN 5.6 0.5 + - - +
87A LEU 4.3 16.4 + - - -
88A THR* 5.3 0.4 - - - +
89A ILE* 4.5 22.8 - - + +
92A LEU* 3.6 10.3 - - - +
112A ILE* 3.0 39.3 + - - +
113A LEU* 3.1 13.0 + - + +
115A ARG* 1.3 82.5 - - + +
117A MET* 1.3 61.0 + - - +
119A ASN* 3.8 13.6 + - - +
120A TRP* 4.1 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE* 3.1 32.1 - - + -
113A LEU* 2.9 29.7 + - + +
114A GLN 3.8 2.7 - - - +
115A ARG 3.2 0.2 - - - -
116A GLN* 1.3 76.5 - - - +
118A GLU* 1.3 64.9 + - - +
119A ASN 3.2 1.1 - - - -
120A TRP* 3.4 29.3 - - + +
135A PRO* 4.2 9.6 - - + +
138A ALA* 3.3 22.7 - - + -
139A ILE* 4.0 21.8 - - + +
142A LEU* 3.9 12.8 - - + -
153A ILE* 3.3 40.1 - - + +
156A ARG* 3.7 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLN* 3.3 23.4 + - + +
115A ARG* 3.9 15.1 + - - +
116A GLN 3.5 0.6 - - - -
117A MET* 1.3 76.4 - - - +
119A ASN* 1.3 66.1 + - - +
120A TRP 2.9 6.2 + - - -
153A ILE* 4.5 7.9 - - + -
156A ARG* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ARG* 3.9 16.9 + - - +
116A GLN* 3.8 12.5 + - - +
117A MET 3.2 0.6 - - - -
118A GLU* 1.3 84.1 - - - +
120A TRP* 1.3 57.6 + - - +
121A ALA* 3.9 3.2 + - - +
156A ARG* 5.0 0.2 - - - -
----------------------------------------------------------
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