Contacts of the helix formed by residues 94 - 107 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92D TRP* 3.5 16.9 - - + -
93D LYS* 1.3 75.7 - - - +
95D THR* 1.3 66.4 + - - +
96D LEU* 4.1 4.0 - - + +
97D LYS* 2.8 48.3 + - + +
98D VAL* 3.1 9.9 + - - +
170D LYS* 4.7 12.8 - - - +
173D ASP* 3.5 24.9 - - - +
272D ARG* 2.8 43.8 + - - -
273D ASN* 4.9 7.1 + - - +
812D TAD 3.5 9.2 - - - +
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Residues in contact with THR 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D CYS* 4.5 13.2 - - + +
86D GLU* 5.6 1.0 + - - -
93D LYS 3.4 2.9 + - - -
94D GLU* 1.3 69.9 - - - +
96D LEU* 1.3 57.6 + - - +
98D VAL* 3.2 10.6 + - - +
99D LEU* 2.9 29.4 + - + +
153D LEU* 3.9 37.7 - - + -
159D LEU* 5.8 1.4 - - + +
169D TRP* 3.7 11.0 - - + -
177D ILE* 4.1 10.5 - - + -
812D TAD 2.8 49.3 + - - -
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Residues in contact with LEU 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D GLU* 3.0 3.1 - - + +
95D THR* 1.3 80.5 - - - +
97D LYS* 1.3 57.1 + - + +
99D LEU* 3.5 3.4 + - - +
100D ARG* 3.0 52.9 + - - +
173D ASP* 3.4 36.6 - - - +
176D GLN* 3.8 36.1 - - + +
177D ILE* 4.0 24.2 - - + +
181D TYR* 3.7 28.5 - - + +
812D TAD 4.4 1.0 + - - -
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Residues in contact with LYS 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D TRP* 4.6 4.8 - - + -
93D LYS* 4.2 29.4 - - + +
94D GLU* 2.8 45.9 + - + +
96D LEU* 1.3 75.7 - - + +
98D VAL* 1.3 57.7 + - - +
100D ARG* 3.1 21.2 + - - +
101D HIS* 2.7 36.5 + - - +
170D LYS* 5.8 4.7 - - - +
272D ARG* 4.8 4.0 - - - +
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Residues in contact with VAL 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D LEU* 4.0 5.2 - - + -
14D CYS* 3.8 15.5 - - - -
49D SER* 4.1 5.4 - - - +
85D TRP* 4.0 10.8 - - + -
86D GLU* 3.4 50.3 - - + +
93D LYS* 4.1 13.5 - - + +
94D GLU 3.1 14.1 + - - +
95D THR* 3.5 9.6 - - - +
97D LYS* 1.3 75.9 - - - +
99D LEU* 1.3 62.5 + - - +
101D HIS* 3.4 0.9 + - - +
102D HIS* 3.1 45.1 + - + +
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Residues in contact with LEU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D LEU* 3.5 26.0 - - + -
95D THR* 2.9 30.0 + - + +
96D LEU* 3.8 4.7 - - - +
98D VAL* 1.3 76.4 - - - +
100D ARG* 1.3 57.5 + - - +
102D HIS* 3.3 5.0 + - - +
103D GLN* 2.9 28.6 + - - +
151D VAL* 3.9 18.1 - - + +
152D LYS 4.3 0.4 - - - -
153D LEU* 4.0 26.2 - - + +
177D ILE* 3.8 37.9 - - + -
181D TYR* 3.8 30.2 - - + -
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Residues in contact with ARG 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D LEU* 3.0 41.4 + - - +
97D LYS* 3.5 27.3 - - - +
99D LEU* 1.3 72.0 - - - +
101D HIS* 1.3 68.8 + - - +
103D GLN* 3.1 2.5 + - + +
104D GLU* 2.9 48.6 + - + +
176D GLN* 3.2 26.5 + - - +
181D TYR* 3.5 23.2 + - - +
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Residues in contact with HIS 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D TRP* 3.2 70.4 - + + +
97D LYS 2.7 19.8 + - - +
98D VAL 3.5 4.9 - - - +
100D ARG* 1.3 73.7 - - - +
102D HIS* 1.3 77.7 + + - +
104D GLU* 3.2 11.1 + - - +
105D LYS* 2.8 44.3 + - + +
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Residues in contact with HIS 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 4.2 16.2 - - + +
47D ILE* 4.0 20.5 - - + +
49D SER* 4.8 3.6 + - - -
83D ASP* 3.1 48.7 + - + +
85D TRP* 4.8 2.4 - - - +
86D GLU 5.6 0.4 + - - -
98D VAL* 3.1 40.9 + - + +
99D LEU* 3.8 3.6 - - - +
101D HIS* 1.3 93.7 - + - +
103D GLN* 1.3 67.6 + - - +
105D LYS* 3.4 13.2 + - - +
106D LEU* 3.2 27.8 + - + +
151D VAL* 4.0 18.2 - - + -
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Residues in contact with GLN 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D LEU 2.9 17.1 + - - +
100D ARG* 3.1 5.3 + - + +
102D HIS* 1.3 75.6 - - - +
104D GLU* 1.3 64.9 + - + +
106D LEU* 3.2 9.8 + - - +
107D GLU* 3.2 30.9 + - - +
148D VAL* 4.2 12.3 + - - +
149D PRO 3.0 23.4 + - - -
150D LYS* 3.7 8.3 - - - +
151D VAL* 2.8 36.0 + - + +
181D TYR* 4.0 20.4 - - + +
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Residues in contact with GLU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ARG* 2.9 42.7 + - + +
101D HIS* 3.5 10.4 + - - +
103D GLN* 1.3 78.1 - - + +
105D LYS* 1.3 57.8 + - - +
107D GLU* 2.8 45.4 + - - +
108D ALA* 4.0 1.9 + - - +
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Residues in contact with LYS 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LYS* 6.3 0.9 - - - +
47D ILE* 6.5 0.2 - - - -
83D ASP* 2.7 29.0 + - - -
85D TRP* 5.9 0.8 - - - +
101D HIS* 2.8 39.7 + - + +
102D HIS* 3.7 18.8 - - - +
103D GLN 3.3 0.2 - - - -
104D GLU* 1.3 72.6 - - - +
106D LEU* 1.3 64.1 + - + +
108D ALA* 3.4 22.0 + - - +
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D VAL* 3.8 22.9 - - + -
45D LYS* 3.8 25.8 - - - +
47D ILE* 5.7 3.1 - - + -
102D HIS* 3.2 10.9 + - + +
103D GLN* 3.2 7.8 + - - +
104D GLU 3.1 1.0 - - - -
105D LYS* 1.3 77.7 - - + +
107D GLU* 1.3 57.4 + - - +
108D ALA 3.0 15.4 + - - +
148D VAL* 3.9 17.5 - - + +
149D PRO* 3.5 28.1 - - + +
151D VAL* 3.5 29.2 - - + -
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Residues in contact with GLU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D GLN* 3.2 29.9 + - - +
104D GLU* 2.8 29.4 + - - +
106D LEU* 1.3 75.5 - - - +
108D ALA* 1.3 58.1 + - - +
148D VAL* 3.9 26.6 - - + +
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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