Contacts of the helix formed by residues 94 - 107 (chain C) in PDB entry 1KR2
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 GLU 94 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C TRP* 3.7 17.1 - - + -
93C LYS* 1.3 75.9 - - - +
95C THR* 1.3 66.5 + - - +
96C LEU* 4.1 4.0 - - + +
97C LYS* 2.9 52.4 + - + +
98C VAL* 3.1 9.4 + - - +
170C LYS* 5.0 12.3 + - + +
173C ASP* 3.6 23.1 - - - +
272C ARG* 2.8 39.2 + - - -
273C ASN* 5.0 6.4 - - - +
811C TAD 3.5 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C CYS* 4.1 13.7 - - + +
86C GLU* 5.8 0.7 - - - -
93C LYS 3.6 1.4 + - - -
94C GLU* 1.3 71.4 - - - +
96C LEU* 1.3 63.4 + - - -
98C VAL* 3.0 10.5 + - - +
99C LEU* 2.9 29.3 + - + +
153C LEU* 3.7 39.5 - - + -
169C TRP* 3.5 12.8 - - + -
177C ILE* 4.5 1.3 - - + -
811C TAD 2.7 52.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLU* 3.1 2.9 - - + +
95C THR* 1.3 80.2 - - - +
97C LYS* 1.3 58.8 + - + +
99C LEU* 3.3 8.1 + - - +
100C ARG* 2.9 55.1 + - - +
173C ASP* 3.3 37.9 - - - +
176C GLN* 3.7 33.9 - - + +
177C ILE* 4.2 19.7 - - + +
181C TYR* 3.8 25.8 - - + -
811C TAD 4.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C TRP* 4.5 5.4 - - + -
93C LYS* 4.3 30.3 - - + +
94C GLU* 2.9 42.0 + - + +
96C LEU* 1.3 76.2 - - + +
98C VAL* 1.3 61.7 + - - +
100C ARG* 3.2 25.1 + - - +
101C HIS* 2.8 30.5 + - - +
170C LYS* 5.8 4.9 - - - +
272C ARG* 4.6 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 4.0 4.3 - - + -
14C CYS* 3.8 15.5 - - - -
49C SER* 4.2 4.0 - - - +
85C TRP* 4.0 15.7 - - + -
86C GLU* 3.3 51.6 - - + +
93C LYS* 4.1 7.6 - - + +
94C GLU 3.1 13.0 + - - +
95C THR* 3.0 11.3 + - - +
97C LYS* 1.3 75.3 - - - +
99C LEU* 1.3 65.0 + - - +
101C HIS* 3.1 1.7 + - - +
102C HIS* 3.0 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.8 24.5 - - + -
95C THR* 2.9 30.2 + - + +
96C LEU* 3.5 7.0 - - - +
98C VAL* 1.3 78.0 - - - +
100C ARG* 1.3 57.1 + - - +
102C HIS* 3.3 1.7 + - - -
103C GLN* 2.9 30.0 + - - +
151C VAL* 3.8 15.1 - - + +
152C LYS 4.4 0.4 - - - -
153C LEU* 4.1 27.8 - - + +
177C ILE* 3.8 36.8 - - + -
181C TYR* 4.1 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C LEU* 2.9 50.9 + - - +
97C LYS* 3.5 30.9 - - - +
99C LEU* 1.3 77.2 - - - +
101C HIS* 1.3 63.6 + - - +
103C GLN* 3.2 2.0 + - - +
104C GLU* 2.9 53.6 + - + +
176C GLN* 3.7 13.7 + - - +
181C TYR* 3.4 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ASP* 4.7 0.8 + - - -
85C TRP* 3.2 68.1 + + + +
97C LYS 2.8 16.9 + - - +
98C VAL 3.1 7.8 + - - +
100C ARG* 1.3 73.1 - - - +
102C HIS* 1.3 82.3 + + - +
104C GLU* 3.5 11.5 + - - +
105C LYS* 3.1 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL* 6.3 0.2 - - + -
12C LEU* 4.0 14.1 - - + +
47C ILE* 3.7 25.9 - - + +
49C SER* 4.8 3.2 + - - -
83C ASP* 3.4 44.9 + - + +
85C TRP* 4.9 1.6 - - - +
98C VAL* 3.0 44.9 + - + +
99C LEU 3.9 3.4 - - - +
101C HIS* 1.3 89.0 - + - +
103C GLN* 1.3 65.2 + - - +
105C LYS* 3.4 14.3 + - - +
106C LEU* 3.1 28.8 + - + +
151C VAL* 4.3 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LEU 2.9 16.9 + - - +
100C ARG* 3.2 3.1 + - - +
102C HIS* 1.3 77.0 - - - +
104C GLU* 1.3 65.1 + - + +
106C LEU* 3.1 12.3 + - - +
107C GLU* 3.1 36.7 + - - +
148C VAL* 3.7 8.1 + - - +
149C PRO 3.0 23.2 + - - -
150C LYS* 3.5 7.9 - - - +
151C VAL* 2.9 37.7 + - + +
181C TYR* 3.8 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C ARG* 2.9 46.0 + - + +
101C HIS* 3.8 10.1 - - - +
103C GLN* 1.3 76.7 - - + +
105C LYS* 1.3 64.3 + - - +
107C GLU* 2.9 32.7 + - - +
108C ALA* 4.2 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LYS* 5.6 8.3 - - - +
47C ILE* 5.8 2.6 - - - +
83C ASP* 3.0 28.1 + - - -
101C HIS* 3.1 34.9 + - + +
102C HIS* 3.5 18.1 + - - +
104C GLU* 1.3 77.6 - - - +
106C LEU* 1.3 62.6 + - + +
108C ALA* 3.2 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL* 3.8 37.5 - - + -
45C LYS* 4.6 16.6 - - - +
47C ILE* 6.3 0.7 - - + -
102C HIS* 3.1 20.7 + - + +
103C GLN* 3.1 10.3 + - - +
105C LYS* 1.3 71.7 - - + +
107C GLU* 1.3 56.8 + - - +
108C ALA 2.9 17.6 + - - +
148C VAL* 3.8 26.1 - - + +
149C PRO* 3.9 28.3 - - + +
151C VAL* 4.3 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C GLN* 3.1 40.3 + - - +
104C GLU* 2.9 24.1 + - - +
106C LEU* 1.3 74.8 - - - +
108C ALA* 1.3 58.0 + - - +
148C VAL* 3.9 25.2 - - + +
----------------------------------------------------------
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