Contacts of the helix formed by residues 21 - 39 (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 GLY 21 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C CYS* 3.1 1.6 - - - +
20C GLU* 1.3 76.0 - - - +
22C LEU* 1.3 65.4 + - - +
23C PRO* 3.3 2.8 - - - +
24C GLU* 3.2 27.6 + - - +
25C LYS* 3.0 29.7 + - - +
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Residues in contact with LEU 22 (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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5C MET* 5.2 8.1 - - + -
6C THR* 4.6 14.4 - - + -
9C ILE* 4.6 20.2 - - + -
16C THR 4.3 4.9 - - - +
17C ASP* 3.3 33.7 - - + +
19C CYS 2.9 19.3 + - - +
20C GLU* 3.1 9.4 - - + +
21C GLY* 1.3 77.6 - - - +
23C PRO* 1.3 69.6 - - + +
25C LYS* 2.9 27.9 + - - +
26C ARG* 3.1 28.8 + - - +
72C TYR* 3.8 18.1 - - + +
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Residues in contact with PRO 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ASP 3.7 3.1 - - - +
18C MET* 3.3 43.7 - - + +
19C CYS* 3.7 13.5 - - - +
21C GLY 3.5 2.7 - - - -
22C LEU* 1.3 96.3 - - + +
24C GLU* 1.3 71.5 - - - +
26C ARG* 3.4 16.5 + - - +
27C LEU* 3.2 21.3 + - - +
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Residues in contact with GLU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLY* 3.5 25.9 + - - +
22C LEU 3.2 1.0 - - - -
23C PRO* 1.3 88.8 - - - +
25C LYS* 1.3 61.9 + - + +
27C LEU* 3.3 3.1 + - - +
28C ARG* 2.8 66.4 + - - +
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Residues in contact with LYS 25 (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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20C GLU 6.1 0.9 - - - -
21C GLY 3.0 18.7 + - - +
22C LEU* 2.9 19.5 + - - +
24C GLU* 1.3 78.3 - - + +
26C ARG* 1.3 63.5 + - - +
28C ARG* 3.2 11.7 + - - +
29C GLY* 3.0 18.7 + - - -
72C TYR* 3.7 25.4 - - + +
74C SER* 4.8 16.0 + - - +
75C ASN* 5.5 6.3 + - - +
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Residues in contact with ARG 26 (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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17C ASP* 2.9 36.2 + - - +
18C MET* 3.6 19.0 - - - +
22C LEU* 3.1 18.0 + - - +
23C PRO* 3.7 17.3 - - - +
25C LYS* 1.3 74.3 - - - +
27C LEU* 1.3 52.6 + - - +
29C GLY* 3.3 0.6 + - - +
30C LYS* 2.6 52.4 + - - +
71C SER* 3.6 19.0 - - - +
72C TYR* 3.0 41.4 + - + +
205C 147 3.3 33.4 + - - -
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PRO* 4.1 30.5 - - + +
42B SER* 4.3 13.7 - - - +
44B VAL* 5.5 4.9 - - + -
23C PRO 3.2 9.6 + - - +
24C GLU* 3.5 8.5 - - - +
25C LYS 3.2 0.4 - - - -
26C ARG* 1.3 76.6 - - - +
28C ARG* 1.3 86.3 + - - +
30C LYS* 3.8 4.4 - - - +
31C THR* 2.6 40.8 + - - +
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Residues in contact with ARG 28 (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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24C GLU* 2.8 72.6 + - - +
25C LYS* 3.6 9.5 - - - +
27C LEU* 1.3 97.9 - - - +
29C GLY* 1.3 63.7 - - - +
31C THR* 3.2 8.2 - - - +
32C LEU* 3.1 31.0 + - + +
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Residues in contact with GLY 29 (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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25C LYS 3.0 11.7 + - - -
26C ARG 3.6 2.5 - - - -
28C ARG* 1.3 73.0 - - - +
30C LYS* 1.3 62.7 + - - +
31C THR 2.8 5.6 + - - -
32C LEU* 2.8 22.2 + - - +
33C MET* 2.9 12.3 + - - +
54C MET* 6.1 0.4 - - - -
70C PHE* 4.0 9.6 - - - -
72C TYR 3.7 22.7 - - - -
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Residues in contact with LYS 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PRO* 3.4 26.2 - - + +
47B ARG* 6.0 2.2 - - - +
65B GLU* 3.8 27.7 + - - +
86B PHE* 3.7 15.0 - - - -
26C ARG* 2.6 35.3 + - - +
27C LEU* 4.0 4.7 - - - +
29C GLY* 1.3 70.1 - - - -
31C THR* 1.3 55.0 + - - +
33C MET* 3.7 25.1 - - + +
34C TYR* 3.0 21.7 + - - +
70C PHE* 3.4 27.7 + - + +
71C SER* 3.6 22.4 + - - +
205C 147 5.5 2.4 + - - -
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Residues in contact with THR 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B HIS* 4.1 22.7 - - + +
41B PRO* 3.9 16.9 - - - +
42B SER* 5.4 0.5 + - - -
27C LEU* 2.6 30.9 + - - +
28C ARG* 3.2 9.9 - - - +
29C GLY 2.8 1.8 + - - -
30C LYS* 1.3 74.9 - - - +
32C LEU* 1.3 68.6 + - + +
34C TYR* 3.2 4.9 + - - +
35C GLU* 3.2 30.8 + - - +
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ARG* 3.1 20.0 + - + +
29C GLY* 2.8 9.4 + - - +
31C THR* 1.3 82.4 - - + +
33C MET* 1.3 63.8 + - - +
35C GLU* 3.1 14.8 + - - +
36C PHE* 3.1 21.8 + - - +
50C LEU* 3.8 24.6 - - + +
53C GLU* 4.2 28.5 - - + +
54C MET* 4.0 31.9 - - + +
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Residues in contact with MET 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLU* 5.7 0.4 - - - +
66B PRO 5.2 2.9 - - - +
86B PHE* 3.7 21.3 - - + -
29C GLY 2.9 11.3 + - - +
30C LYS* 3.7 23.1 - - + +
32C LEU* 1.3 77.8 - - - +
34C TYR* 1.3 52.8 + - + +
36C PHE* 3.1 8.7 + - - +
37C ASN* 2.8 38.0 + - - +
54C MET* 4.3 2.0 - - - -
68C VAL* 3.3 25.8 - - + +
69C TYR* 3.8 15.0 - - + -
70C PHE* 3.5 55.7 - - + +
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Residues in contact with TYR 34 (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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37B ASN 5.7 0.2 - - - -
38B HIS 3.5 22.8 + - - -
39B SER 4.1 5.4 - - - -
40B HIS* 3.5 41.4 + + - +
41B PRO* 3.8 20.4 - - + -
47B ARG* 5.9 0.4 - - - -
30C LYS 3.0 18.8 + - - +
31C THR 3.4 5.6 - - - +
32C LEU 3.2 0.4 - - - -
33C MET* 1.3 77.5 - - + +
35C GLU* 1.3 77.7 + - + +
37C ASN* 3.4 3.8 + - - +
38C HIS* 3.0 74.9 + + + +
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Residues in contact with GLU 35 (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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40B HIS* 4.6 8.7 + - - -
31C THR* 3.2 20.0 + - - +
32C LEU* 3.1 17.1 + - - +
34C TYR* 1.3 92.1 - - + +
36C PHE* 1.3 59.9 + - - +
38C HIS* 3.4 3.0 + - - -
39C SER* 3.0 28.9 + - - -
46C LYS* 4.0 22.8 + - - +
50C LEU* 4.0 17.7 - - + +
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Residues in contact with PHE 36 (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 3.1 9.2 + - - +
33C MET* 3.4 8.7 - - - +
35C GLU* 1.3 79.1 - - - +
37C ASN* 1.3 77.1 + - - +
39C SER* 3.0 22.0 + - - +
47C ARG* 3.5 36.3 - - + -
50C LEU* 3.7 24.5 - - + -
51C ILE* 4.0 6.5 - - + -
54C MET* 3.4 33.7 - - + -
64C VAL* 3.5 30.7 - - + -
66C PRO* 3.6 34.2 - - + +
68C VAL* 3.9 10.1 - - + -
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Residues in contact with ASN 37 (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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34A TYR* 5.5 0.3 - - - -
38A HIS* 4.3 12.8 + - - -
33C MET* 2.8 28.8 + - - +
34C TYR* 3.4 5.1 + - - +
36C PHE* 1.3 87.6 - - - +
38C HIS* 1.3 68.0 + - + +
39C SER 3.5 3.3 + - - +
47C ARG* 5.8 0.3 + - - -
66C PRO* 3.8 8.7 - - - +
67C PRO* 3.3 20.4 - - + +
68C VAL 2.9 45.1 + - - +
69C TYR* 3.9 10.4 - - - +
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Residues in contact with HIS 38 (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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34A TYR* 3.7 19.1 + - - -
38A HIS* 3.5 28.0 + + - -
37B ASN 4.6 10.2 + - - -
38B HIS* 3.6 25.2 + + - -
34C TYR* 3.0 68.6 + + + +
35C GLU* 3.7 4.0 - - - +
37C ASN* 1.3 84.0 - - + +
39C SER* 1.3 64.8 + - - +
40C HIS 3.7 0.5 + - - -
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Residues in contact with SER 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 4.0 7.6 - - - -
35C GLU 3.0 15.3 + - - -
36C PHE* 3.0 13.6 + - - +
37C ASN 4.5 2.4 - - - +
38C HIS* 1.3 81.1 - - - +
40C HIS* 1.3 62.8 + - - +
41C PRO* 3.8 0.5 - - - +
43C GLU* 3.7 16.2 - - - -
46C LYS* 4.0 15.7 - - - +
47C ARG* 2.8 51.1 + - - +
50C LEU* 5.1 0.2 - - - -
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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
------------------------------------------------------------
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