Contacts of the helix formed by residues 34 - 46 (chain B) in PDB entry 2KI4
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 SER 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B GLU* 4.6 15.0 - - - -
28B GLY 5.9 1.6 - - - -
32B SER* 3.8 1.6 + - - -
33B LEU* 1.3 73.3 - - - +
35B VAL* 1.3 66.0 + - - +
36B ASN 3.4 1.6 - - - -
37B GLU* 2.9 21.9 + - - +
38B PHE* 2.7 32.9 + - - +
69B SER* 3.2 21.5 + - - -
70B GLU* 4.9 4.5 - - - +
71B LEU* 5.5 0.9 - - - -
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Residues in contact with VAL 35 (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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34B SER* 1.3 83.2 + - - +
36B ASN* 1.3 58.3 + - - +
38B PHE* 3.2 6.0 + - - +
39B LYS* 2.9 28.8 + - + +
56B LEU* 4.3 13.3 - - + +
60B MET* 4.8 19.1 - - + -
69B SER* 4.3 24.0 - - - +
71B LEU* 6.0 2.0 - - + -
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Residues in contact with ASN 36 (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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27B GLU* 3.6 18.4 + - - +
34B SER* 3.4 0.8 - - - -
35B VAL* 1.3 77.1 - - - +
37B GLU* 1.3 54.2 + - - +
39B LYS* 2.9 10.1 + - - +
40B GLU* 2.8 63.9 + - - +
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Residues in contact with GLU 37 (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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23B PHE* 2.8 16.2 - - - +
24B ALA 2.6 27.7 - - - +
26B GLN* 3.5 17.3 - - + -
27B GLU* 3.0 41.7 + - - +
28B GLY 4.3 4.0 - - - +
32B SER 3.3 9.4 - - - +
33B LEU* 3.8 16.3 - - + +
34B SER* 2.9 36.7 + - - +
36B ASN* 1.3 76.7 - - - +
38B PHE* 1.3 63.5 + - - +
40B GLU* 3.4 22.9 + - - +
41B LEU* 3.6 4.2 + - - +
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Residues in contact with PHE 38 (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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33B LEU* 3.9 13.2 - - + +
34B SER 2.7 21.2 + - - +
35B VAL* 3.4 6.1 - - - +
37B GLU* 1.3 68.6 - - - +
39B LYS* 1.3 66.2 + - - +
41B LEU* 2.9 23.1 + - + +
42B VAL* 3.7 7.0 + - + +
56B LEU* 3.5 39.5 - - + -
59B LYS* 4.5 3.1 - - + -
60B MET* 4.7 7.2 - - + -
63B LEU* 3.3 35.0 - - + -
71B LEU* 4.3 20.0 - - + -
76B TYR* 3.7 34.3 - + - -
79B LEU* 3.8 30.7 - - + -
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Residues in contact with LYS 39 (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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35B VAL* 2.9 14.6 + - + +
36B ASN* 3.5 10.3 - - - +
38B PHE* 1.3 75.9 - - - +
40B GLU* 1.3 57.9 + - + +
42B VAL* 3.0 10.7 - - + +
43B THR* 2.9 45.5 + - - +
53B VAL* 3.0 31.2 + - - +
54B GLY* 3.7 18.6 + - - -
56B LEU* 3.8 32.8 - - + +
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Residues in contact with GLU 40 (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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115A ARG* 3.0 35.1 + - - +
23B PHE* 3.7 15.0 - - + -
26B GLN* 3.4 24.9 + - - +
27B GLU* 6.0 0.2 - - - +
36B ASN* 2.8 39.9 + - - +
37B GLU* 3.4 15.9 - - - +
38B PHE 3.1 0.2 + - - -
39B LYS* 1.3 73.2 - - + +
41B LEU* 1.3 66.2 + - - +
43B THR* 4.5 5.3 - - - -
44B GLN* 3.3 26.1 + - - +
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Residues in contact with LEU 41 (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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19B THR* 4.6 9.6 - - + +
23B PHE* 3.8 37.9 - - + -
33B LEU* 5.9 0.2 - - + -
37B GLU 3.6 5.1 + - - +
38B PHE* 2.9 14.7 + - + +
40B GLU* 1.3 78.0 - - - +
42B VAL* 1.3 66.4 + - + +
45B GLN* 3.0 38.7 + - + +
46B LEU* 3.7 15.6 + - + -
76B TYR* 3.6 34.3 - - + +
79B LEU* 4.4 16.8 - - + -
83B LEU* 5.5 3.8 - - + -
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Residues in contact with VAL 42 (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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38B PHE* 4.0 4.7 - - + +
39B LYS* 3.0 23.6 - - + +
41B LEU* 1.3 79.8 - - + +
43B THR* 1.3 66.0 + - - +
46B LEU* 2.8 61.6 + - + +
50B LEU* 4.9 14.4 - - + +
52B ASP 5.5 6.3 - - - +
53B VAL* 4.5 6.7 - - + +
56B LEU* 3.7 32.8 - - + -
59B LYS* 6.2 2.0 - - + -
79B LEU* 4.5 19.1 - - + -
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Residues in contact with THR 43 (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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39B LYS* 2.9 40.6 + - - +
40B GLU* 4.5 4.3 - - - -
42B VAL* 1.3 77.2 - - - +
44B GLN* 1.3 58.6 - - - +
46B LEU 5.5 0.4 - - - -
47B PRO* 5.8 3.1 - - - +
53B VAL* 4.1 22.0 - - + +
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Residues in contact with GLN 44 (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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115A ARG* 4.2 15.0 - - - +
23B PHE* 3.6 30.8 - - + -
40B GLU* 3.3 15.9 + - - +
42B VAL 3.1 0.8 - - - -
43B THR* 1.3 79.7 - - - +
45B GLN* 1.3 76.0 + - + +
46B LEU 3.4 2.2 + - - -
47B PRO* 4.7 8.0 - - - +
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Residues in contact with GLN 45 (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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19B THR* 3.4 23.5 + - - +
22B THR* 5.3 0.3 - - - +
23B PHE* 3.1 32.1 - - + -
41B LEU* 3.0 19.8 + - + +
44B GLN* 1.3 91.3 - - + +
46B LEU* 1.3 69.5 + - - +
47B PRO* 3.8 7.4 - - - +
8C GLU* 4.8 11.1 + - - -
9C LEU* 4.3 19.7 - - + +
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Residues in contact with LEU 46 (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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41B LEU* 4.2 9.2 - - + +
42B VAL* 2.8 52.1 + - + +
44B GLN 3.4 1.0 - - - -
45B GLN* 1.3 84.5 - - - +
47B PRO* 1.3 62.9 - - + +
48B HIS 3.6 0.7 - - - +
49B LEU* 4.0 24.9 - - + +
50B LEU* 3.5 33.7 - - + +
53B VAL* 4.6 3.6 - - - +
79B LEU* 5.1 0.7 - - + -
83B LEU* 3.7 42.6 - - + -
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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