Contacts of the helix formed by residues 94 - 107 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B TRP* 3.5 18.3 - - + -
93B LYS* 1.3 75.4 - - - +
95B THR* 1.3 66.4 + - - +
96B LEU* 4.0 4.0 - - + +
97B LYS* 2.7 54.3 + - + +
98B VAL* 3.0 9.0 + - - +
170B LYS* 4.5 18.0 + - + +
173B ASP* 3.6 22.4 - - - +
272B ARG* 2.9 37.4 + - - -
273B ASN* 5.1 4.0 - - - +
810B TAD 3.4 13.5 - - - +
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Residues in contact with THR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B CYS* 4.4 12.6 - - + +
86B GLU* 5.8 0.4 - - - -
93B LYS 3.5 3.0 + - - -
94B GLU* 1.3 70.9 - - - +
96B LEU* 1.3 57.2 + - - +
98B VAL* 3.0 11.0 + - - +
99B LEU* 2.9 35.1 + - + +
153B LEU* 4.0 37.5 - - + -
159B LEU* 5.6 0.9 - - + +
169B TRP* 3.6 11.1 - - + -
177B ILE* 4.2 5.8 - - + -
810B TAD 2.8 48.9 + - - -
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLU* 3.0 2.9 - - + +
95B THR* 1.3 80.1 - - - +
97B LYS* 1.3 58.6 + - + +
99B LEU* 3.5 2.5 + - - +
100B ARG* 2.9 53.3 + - - +
173B ASP* 3.6 35.7 - - - +
176B GLN* 3.8 32.8 - - + +
177B ILE* 4.1 25.3 - - + +
181B TYR* 3.6 28.9 - - + -
810B TAD 4.4 0.8 + - - -
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Residues in contact with LYS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B TRP* 4.6 5.3 - - + -
93B LYS* 4.1 30.8 - - + +
94B GLU* 2.7 48.4 + - + +
96B LEU* 1.3 75.3 - - + +
98B VAL* 1.3 53.2 + - - +
100B ARG* 3.2 21.0 + - - +
101B HIS* 2.7 37.4 + - - +
170B LYS* 5.3 7.4 - - - +
272B ARG* 4.1 7.9 - - - +
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 4.0 4.5 - - + -
14B CYS* 3.8 17.0 - - - -
49B SER* 4.1 7.2 - - - +
85B TRP* 4.0 16.8 - - + -
86B GLU* 3.5 46.4 - - + +
93B LYS* 4.1 8.3 - - + +
94B GLU 3.0 13.9 + - - +
95B THR* 3.0 8.3 + - - +
97B LYS* 1.3 76.6 - - - +
99B LEU* 1.3 62.0 + - - +
101B HIS* 3.3 0.9 + - - +
102B HIS* 3.1 40.8 + - + +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.5 25.1 - - + -
95B THR* 2.9 27.5 + - + +
96B LEU* 3.8 3.8 - - - +
98B VAL* 1.3 76.5 - - - +
100B ARG* 1.3 58.2 + - - +
102B HIS* 3.4 2.1 + - - +
103B GLN* 2.9 29.1 + - - +
151B VAL* 3.9 18.2 - - + +
152B LYS 4.3 0.2 - - - -
153B LEU* 3.9 27.4 - - + +
177B ILE* 3.9 39.5 - - + -
181B TYR* 3.7 31.3 - - + -
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 2.9 41.3 + - - +
97B LYS* 3.6 27.0 - - - +
99B LEU* 1.3 75.4 - - - +
101B HIS* 1.3 66.4 + - - +
103B GLN* 3.9 1.3 - - + +
104B GLU* 2.9 53.4 + - + +
176B GLN* 3.4 24.2 + - - -
181B TYR* 3.3 22.0 + - - +
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Residues in contact with HIS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B TRP* 3.1 72.1 - + + +
97B LYS 2.7 20.2 + - - +
98B VAL 3.5 4.7 - - - +
100B ARG* 1.3 74.6 - - - +
102B HIS* 1.3 74.9 + + - +
104B GLU* 3.2 9.3 + - - +
105B LYS* 3.0 45.9 + - + +
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Residues in contact with HIS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 4.4 12.8 - - + +
47B ILE* 4.0 24.4 - - + +
49B SER* 4.9 3.2 + - - -
83B ASP* 3.2 46.9 + - + +
85B TRP* 4.9 2.0 - + - +
86B GLU 5.9 0.2 + - - -
98B VAL* 3.1 39.2 + - + +
99B LEU* 3.8 4.0 - - - +
101B HIS* 1.3 89.3 - + - +
103B GLN* 1.3 65.2 + - - +
105B LYS* 3.4 21.0 + - - +
106B LEU* 3.2 26.3 + - - +
151B VAL* 4.0 17.5 - - + -
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Residues in contact with GLN 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU 2.9 17.7 + - - +
100B ARG* 3.3 5.1 + - - +
102B HIS* 1.3 76.3 - - - +
104B GLU* 1.3 63.7 + - + +
106B LEU* 3.3 11.6 + - - +
107B GLU* 3.3 23.8 + - - +
148B VAL* 4.0 13.1 + - - +
149B PRO 3.0 21.8 + - - -
150B LYS* 3.6 8.2 - - - +
151B VAL* 2.9 33.6 + - + +
181B TYR* 3.8 20.7 - - + +
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ARG* 2.9 43.3 + - + +
101B HIS* 3.6 6.7 - - - +
103B GLN* 1.3 73.9 - - + +
105B LYS* 1.3 62.0 + - - +
107B GLU* 2.8 44.7 + - - +
108B ALA* 4.7 0.3 - - - +
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Residues in contact with LYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ASP* 2.9 31.3 + - - -
85B TRP* 5.7 0.4 - - - +
101B HIS* 3.0 35.2 + - + +
102B HIS* 3.6 19.7 - - - +
104B GLU* 1.3 77.1 - - - +
106B LEU* 1.3 63.8 + - + +
107B GLU 4.2 0.3 - - - -
108B ALA* 4.1 15.7 + - - +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 3.7 26.5 - - + -
45B LYS* 5.0 13.5 - - - +
47B ILE* 6.0 3.1 - - + -
102B HIS* 3.2 12.8 + - + +
103B GLN* 3.6 7.9 - - - +
104B GLU 3.1 1.2 - - - -
105B LYS* 1.3 81.5 - - + +
107B GLU* 1.3 59.0 + - - +
108B ALA 2.9 14.2 + - - +
148B VAL* 4.1 18.6 - - + +
149B PRO* 3.6 33.2 - - + +
151B VAL* 3.7 23.1 - - + -
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B GLN* 3.3 31.1 + - - +
104B GLU* 2.8 23.7 + - - +
106B LEU* 1.3 74.1 - - - +
108B ALA* 1.3 65.6 + - - +
148B VAL* 3.7 30.4 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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