Contacts of the helix formed by residues 113 - 122 (chain A) in PDB entry 6JKG
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 ASN 113 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A SER* 3.0 21.2 + - - +
112A ASN* 1.3 74.1 - - - +
114A LYS* 1.3 66.4 + - - +
115A GLU* 3.4 9.7 + - - +
116A LEU* 3.1 40.3 + - + +
117A PHE* 3.3 14.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASN* 3.1 33.8 + - - +
113A ASN* 1.3 74.7 + - - +
115A GLU* 1.3 78.0 + - - +
117A PHE* 3.4 14.7 + - - +
118A TYR 3.5 0.2 + - - -
171A TYR* 3.1 65.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASN* 3.4 6.6 - - - +
114A LYS* 1.3 90.8 + - - +
116A LEU* 1.3 55.3 + - - +
117A PHE 3.4 0.2 - - - -
118A TYR* 3.2 13.1 + - + +
119A ARG* 2.8 60.0 + - - +
171A TYR* 4.8 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PRO* 3.7 26.5 - - + -
108A PRO* 5.5 1.8 - - + -
111A SER* 3.6 25.4 - - - +
113A ASN* 3.1 29.6 + - + +
115A GLU* 1.3 74.0 - - - +
117A PHE* 1.3 69.1 + - + +
119A ARG* 2.9 18.1 + - - +
120A VAL* 2.9 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PRO* 3.9 21.3 - - + -
108A PRO 3.3 23.1 - - - -
109A PRO 3.8 7.0 - - - -
111A SER* 4.1 7.0 - - - -
112A ASN* 3.2 48.2 - - - -
113A ASN 3.3 12.1 + - - -
114A LYS* 3.4 12.8 - - - +
116A LEU* 1.3 76.1 - - + +
118A TYR* 1.3 57.2 + - - +
121A ASN* 3.1 38.9 + - - +
171A TYR* 4.5 3.1 - + + -
172A TYR* 3.6 45.5 - + + -
175A THR* 3.6 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LYS 3.5 1.8 + - - -
115A GLU* 3.2 15.0 + - + +
116A LEU 3.1 0.6 - - - -
117A PHE* 1.3 76.2 - - - +
119A ARG* 1.3 77.0 + - + +
122A TYR* 3.4 57.3 - + + +
123A ILE* 3.4 19.2 + - + +
171A TYR* 3.7 31.9 - + + +
175A THR* 3.7 7.6 - - + +
178A LEU* 4.4 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A CYS* 4.4 11.2 - - - -
115A GLU* 2.8 48.6 + - - +
116A LEU* 2.9 22.1 + - - +
118A TYR* 1.3 84.6 - - + +
120A VAL* 1.3 65.7 + - + +
123A ILE* 3.3 8.8 + - - +
124A GLY* 2.9 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 3.7 21.2 - - + +
86A CYS* 5.0 6.5 - - - -
103A HIS* 5.1 0.2 + - - -
105A ALA* 3.7 23.2 - - + +
106A SER 5.1 0.2 - - - -
107A PRO* 3.6 29.8 - - + -
116A LEU* 2.9 31.6 + - + +
119A ARG* 1.3 77.2 - - + +
121A ASN* 1.3 67.7 + - - +
124A GLY* 3.7 14.4 - - - +
125A THR* 3.6 7.6 + - - -
179A GLN* 4.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ALA 4.3 0.7 - - - +
106A SER* 3.7 14.6 - - - -
107A PRO* 3.5 18.6 - - - +
117A PHE* 3.1 23.0 + - - +
120A VAL* 1.3 77.5 - - - +
122A TYR* 1.3 55.5 + - - +
125A THR* 2.2 27.8 + - - -
172A TYR* 3.6 23.4 - - - -
175A THR* 3.1 34.5 + - - +
176A LYS* 3.9 9.8 - - - +
179A GLN* 2.9 31.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PHE 4.0 0.2 + - - -
118A TYR* 3.4 47.4 + + + +
120A VAL 3.4 0.2 - - - -
121A ASN* 1.3 77.6 - - + +
123A ILE* 1.3 95.6 + - + +
125A THR* 2.9 16.2 + - - -
126A LYS* 3.0 34.3 + - + +
175A THR* 5.1 2.2 - - - +
178A LEU* 3.7 46.9 - - + -
179A GLN* 4.9 3.4 - - - +
182A ALA* 5.1 7.4 - - + -
----------------------------------------------------------
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