Contacts of the helix formed by residues 43 - 55 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C SER* 3.7 6.4 - - - -
40C HIS* 2.8 47.6 + - - +
42C SER* 1.3 77.4 + - - +
44C VAL* 1.3 56.5 + - - -
45C GLU* 3.4 8.5 - - - +
46C LYS* 3.2 42.6 + - + +
47C ARG* 3.0 30.5 + - - +
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Residues in contact with VAL 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 5.4 5.2 - - + -
41C PRO 3.8 17.7 - - - +
42C SER* 2.6 16.4 + - - +
43C GLU* 1.3 73.5 - - - +
45C GLU* 1.3 65.3 + - + +
47C ARG* 3.6 8.5 - - - +
48C GLU* 3.0 46.9 + - - +
63C TRP* 4.7 21.6 - - + -
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Residues in contact with GLU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C SER 3.9 7.7 - - - +
43C GLU* 3.6 6.1 - - - +
44C VAL* 1.3 86.7 + - + +
46C LYS* 1.3 66.1 + - - +
48C GLU* 2.9 22.6 + - - +
49C SER* 3.0 16.2 + - - -
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Residues in contact with LYS 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLU* 4.0 27.2 - - - +
39C SER* 4.0 15.9 - - - -
43C GLU* 3.2 47.3 + - + +
44C VAL 3.4 0.2 - - - -
45C GLU* 1.3 80.4 + - - +
47C ARG* 1.3 57.1 + - - +
49C SER* 3.3 8.3 + - - -
50C LEU* 3.0 40.6 + - + +
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Residues in contact with ARG 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LYS* 6.0 2.2 - - - +
34A TYR* 5.9 0.4 - - - -
36C PHE* 3.5 23.5 + - + -
37C ASN 5.8 0.4 + - - -
39C SER* 2.8 44.7 + - - +
40C HIS 3.7 4.0 + - - -
41C PRO* 3.7 37.7 + - - +
43C GLU 3.0 22.2 + - - +
44C VAL* 3.6 8.1 - - - +
46C LYS* 1.3 76.3 - - - +
48C GLU* 1.3 54.2 + - - +
50C LEU* 3.2 6.0 + - - +
51C ILE* 2.7 38.1 + - - +
63C TRP* 4.6 23.6 - - + -
64C VAL 5.9 0.4 - - - -
65C GLU* 4.7 6.9 + - - -
66C PRO* 3.5 35.6 - - - +
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Residues in contact with GLU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C VAL* 3.0 33.9 + - - +
45C GLU* 2.9 15.5 + - - +
47C ARG* 1.3 77.4 - - - +
49C SER* 1.3 61.4 + - - +
51C ILE* 3.3 18.6 - - + +
52C LYS* 3.4 31.6 + - + +
62C ALA 5.4 7.2 - - - +
63C TRP* 4.6 14.1 - - + -
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Residues in contact with SER 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C GLU 3.0 16.4 + - - -
46C LYS* 3.3 11.6 + - - -
48C GLU* 1.3 73.3 - - - +
50C LEU* 1.3 65.6 + - - +
52C LYS* 3.2 13.3 + - - +
53C GLU* 3.0 22.9 + - - +
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Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 3.8 42.0 - - + +
35C GLU* 4.0 18.2 - - + +
36C PHE* 3.7 40.6 - - + +
39C SER* 5.1 0.9 - - - -
46C LYS* 3.0 42.4 + - + +
47C ARG* 3.4 7.0 - - - +
48C GLU 3.2 0.2 - - - -
49C SER* 1.3 77.5 - - - +
51C ILE* 1.3 52.8 + - - +
53C GLU* 2.9 5.8 + - - +
54C MET* 2.7 39.9 + - + +
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Residues in contact with ILE 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C PHE* 4.0 12.8 - - + -
47C ARG 2.7 23.3 - - - +
48C GLU* 3.3 11.0 - - + +
50C LEU* 1.3 74.0 - - - +
52C LYS* 1.3 75.4 + - - +
53C GLU 3.2 0.7 + - - -
54C MET* 3.7 18.3 - - + +
55C PHE* 3.2 34.1 + - + -
58C VAL* 3.3 36.0 - - + +
62C ALA* 3.6 21.8 - - + +
64C VAL* 4.7 15.9 - - + +
78C ILE* 5.7 0.4 - - + -
82C PHE* 5.9 0.2 - - + -
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Residues in contact with LYS 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C GLU* 3.4 35.1 + - + +
49C SER* 3.2 13.6 + - - +
50C LEU 3.2 0.8 - - - -
51C ILE* 1.3 100.0 - - - +
53C GLU* 1.3 60.5 + - - +
55C PHE 3.8 10.2 - - - +
58C VAL* 4.0 17.5 - - + +
59C GLY 5.0 11.9 + - - -
60C GLU* 6.3 1.1 - - - +
62C ALA* 5.0 7.7 + - - +
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Residues in contact with GLU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 4.2 28.4 - - + +
49C SER 3.0 11.1 + - - +
50C LEU* 2.9 9.2 + - + +
52C LYS* 1.3 81.1 - - - +
54C MET* 1.3 63.0 + - - +
55C PHE 3.4 3.9 + - - +
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Residues in contact with MET 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLY* 6.1 0.4 - - - -
32C LEU* 4.0 24.4 - - + +
33C MET* 4.3 7.2 - - - -
36C PHE* 3.4 55.6 - - + -
50C LEU* 2.7 20.2 + - - +
51C ILE* 3.7 21.1 - - + -
53C GLU* 1.3 76.7 - - - +
55C PHE* 1.3 74.8 + - + +
64C VAL* 6.0 0.9 - - + -
68C VAL* 4.3 7.9 - - + -
70C PHE* 3.9 30.5 - - + -
72C TYR 4.2 2.9 - - - +
73C GLY* 3.3 23.4 - - - -
74C SER* 3.6 4.0 + - - -
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Residues in contact with PHE 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ILE* 3.2 31.4 + - + +
52C LYS 3.8 14.7 - - - +
53C GLU 4.0 3.5 - - - +
54C MET* 1.3 97.1 - - + +
56C ALA* 1.3 66.7 + - - +
57C THR* 3.3 3.8 + - - +
58C VAL* 3.8 11.9 - - + +
64C VAL* 4.4 19.1 - - + -
68C VAL* 4.6 14.6 - - + -
70C PHE* 3.9 26.5 - + - -
73C GLY 3.4 12.8 - - - -
74C SER* 4.5 1.1 - - - -
76C ILE* 3.7 36.1 - - + +
78C ILE* 3.7 24.5 - - + -
82C PHE* 6.0 0.2 - + - -
88C LEU* 5.9 2.5 - - + -
90C ILE* 5.3 4.5 - - + -
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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