Contacts of the helix formed by residues 43 - 55 (chain B) in PDB entry 1KRV
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 43 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B SER* 4.0 5.8 - - - -
40B HIS* 3.0 44.9 + - - +
41B PRO 4.5 1.1 - - - -
42B SER* 1.3 72.5 + - - +
44B VAL* 1.3 57.2 + - - +
45B GLU* 3.5 10.1 - - - +
46B LYS* 3.1 44.4 + - + +
47B ARG* 3.0 30.4 + - - +
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Residues in contact with VAL 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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41B PRO 3.8 9.9 - - - +
42B SER* 2.4 35.8 + - - +
43B GLU* 1.3 65.5 - - - +
45B GLU* 1.3 70.2 + - + +
47B ARG* 3.6 7.4 - - - +
48B GLU* 2.9 46.9 + - - +
63B TRP* 4.6 18.1 - - + -
27C LEU* 5.5 5.2 - - + -
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Residues in contact with GLU 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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42B SER 4.2 5.0 - - - +
43B GLU* 3.9 6.8 - - - +
44B VAL* 1.3 86.1 + - + +
46B LYS* 1.3 70.4 + - - +
48B GLU* 2.9 20.1 + - - +
49B SER* 3.0 15.3 + - - -
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Residues in contact with LYS 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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35B GLU* 3.8 30.1 + - - +
39B SER* 4.2 9.0 - - - +
43B GLU* 3.1 47.1 + - + +
44B VAL 3.4 0.2 - - - -
45B GLU* 1.3 82.0 + - - +
47B ARG* 1.3 55.7 + - - +
49B SER* 2.9 9.8 + - - +
50B LEU* 2.8 54.0 + - + +
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Residues in contact with ARG 47 (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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36B PHE* 3.5 25.3 - - + -
39B SER* 3.0 44.1 + - - +
40B HIS 3.9 4.0 + - - -
41B PRO* 3.7 33.1 + - - +
43B GLU 3.0 21.5 + - - +
44B VAL* 3.6 7.0 - - - +
46B LYS* 1.3 77.0 - - - +
48B GLU* 1.3 52.6 + - - +
50B LEU* 3.3 3.5 + - - -
51B ILE* 2.7 38.8 + - - +
63B TRP* 4.4 27.5 - - + -
64B VAL 5.5 0.2 - - - -
65B GLU* 4.2 9.7 + - - -
66B PRO* 3.4 36.5 - - - +
30C LYS* 6.0 2.4 - - - +
34C TYR* 5.9 0.4 - - - -
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Residues in contact with GLU 48 (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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44B VAL* 2.9 39.0 + - - +
45B GLU* 2.9 9.6 + - - +
47B ARG* 1.3 79.0 - - - +
49B SER* 1.3 58.9 + - - +
51B ILE* 3.9 5.5 - - + +
52B LYS* 2.9 44.0 + - - +
62B ALA 5.3 8.5 - - - +
63B TRP* 4.5 13.9 - - + -
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Residues in contact with SER 49 (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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45B GLU 3.0 10.6 + - - -
46B LYS* 2.9 19.4 + - - +
48B GLU* 1.3 75.2 - - - +
50B LEU* 1.3 61.5 + - - +
51B ILE 3.3 0.7 - - - -
52B LYS* 3.0 12.1 + - - +
53B GLU* 2.9 29.9 + - - +
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Residues in contact with LEU 50 (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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32B LEU* 4.2 37.2 - - + +
35B GLU* 4.0 9.9 - - + +
36B PHE* 3.6 40.8 - - + +
39B SER* 4.9 1.3 - - - -
46B LYS* 2.8 53.4 + - + +
47B ARG* 3.6 6.1 - - - +
49B SER* 1.3 78.4 + - - +
51B ILE* 1.3 58.2 + - - +
53B GLU* 3.2 5.7 + - + +
54B MET* 2.9 33.3 + - + +
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Residues in contact with ILE 51 (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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36B PHE* 3.8 16.8 - - + -
47B ARG 2.7 21.8 - - - +
48B GLU* 3.9 7.2 - - + +
50B LEU* 1.3 74.9 - - - +
52B LYS* 1.3 74.2 + - - +
54B MET* 3.6 17.7 - - + +
55B PHE* 3.3 34.3 + - + +
58B VAL* 3.4 38.2 - - + +
62B ALA* 3.7 21.1 - - + +
63B TRP* 6.5 0.2 - - - -
64B VAL* 4.4 16.2 - - + +
78B ILE* 5.6 0.7 - - + -
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Residues in contact with LYS 52 (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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48B GLU* 2.9 37.4 + - - +
49B SER* 3.0 14.1 + - - +
51B ILE* 1.3 97.8 - - - +
53B GLU* 1.3 62.5 + - - +
55B PHE 3.7 12.1 - - - +
58B VAL* 4.3 17.7 - - + +
59B GLY 5.4 5.8 + - - -
60B GLU* 6.4 1.1 - - - +
62B ALA* 5.2 7.7 + - - +
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Residues in contact with GLU 53 (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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32B LEU* 3.5 28.6 - - + +
49B SER 2.9 14.8 + - - +
50B LEU* 3.9 6.3 - - + +
51B ILE 3.2 0.2 - - - -
52B LYS* 1.3 81.2 - - - +
54B MET* 1.3 59.9 + - - +
55B PHE 4.6 2.0 - - - +
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Residues in contact with MET 54 (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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29B GLY* 5.4 1.1 - - - +
32B LEU* 4.1 26.7 - - + +
33B MET* 4.4 1.8 - - - -
36B PHE* 3.5 54.5 - - + -
50B LEU 2.9 22.4 + - - +
51B ILE* 3.6 22.9 - - + +
53B GLU* 1.3 78.6 - - - +
55B PHE* 1.3 75.7 + - + +
64B VAL* 5.9 0.9 - - + -
68B VAL* 4.5 8.5 - - + -
70B PHE* 4.0 28.7 - - + -
72B TYR 4.4 1.7 - - - +
73B GLY* 2.8 24.8 - - - +
74B SER* 3.8 2.1 + - - -
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Residues in contact with PHE 55 (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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51B ILE* 3.3 26.1 + - + -
52B LYS 3.7 14.6 - - - +
53B GLU 4.6 1.6 - - - +
54B MET* 1.3 91.2 + - + +
56B ALA* 1.3 66.3 + - - +
57B THR* 3.1 4.6 + - - +
58B VAL* 3.6 20.7 - - + +
64B VAL* 4.4 20.0 - - + -
68B VAL* 4.5 15.3 - - + -
70B PHE* 3.8 28.9 - + - -
73B GLY 3.1 11.2 - - - -
74B SER* 4.9 0.4 - - - -
76B ILE* 3.8 30.7 - - + +
78B ILE* 3.5 27.6 - - + -
82B PHE* 5.4 1.3 - + - -
88B LEU* 6.1 1.8 - - + -
90B ILE* 5.8 4.0 - - + -
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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