Contacts of the helix formed by residues 21 - 39 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A CYS 3.2 1.8 - - - -
20A GLU* 1.3 75.0 - - - +
22A LEU* 1.3 64.3 + - - +
23A PRO* 3.3 2.6 - - - +
24A GLU* 3.1 30.5 + - - +
25A LYS* 2.9 29.1 + - - +
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A MET* 5.0 6.7 - - + -
6A THR* 4.6 18.8 - - + -
9A ILE* 4.6 19.5 - - + -
16A THR 4.5 4.7 - - - +
17A ASP* 3.5 28.7 - - + +
19A CYS 3.1 14.8 - - - +
20A GLU* 3.0 12.2 + - + +
21A GLY* 1.3 76.3 - - - +
23A PRO* 1.3 72.5 - - + +
25A LYS* 2.9 29.5 + - - +
26A ARG* 3.0 29.6 + - - +
72A TYR* 3.9 16.7 - - + +
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Residues in contact with PRO 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASP 3.6 9.4 - - - +
18A MET* 3.5 37.7 - - + +
19A CYS* 3.6 11.7 - - - +
21A GLY 3.5 2.9 - - - +
22A LEU* 1.3 94.8 - - + +
24A GLU* 1.3 73.4 + - - +
26A ARG* 3.1 29.1 + - - +
27A LEU* 3.1 12.5 + - - +
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Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY* 3.1 29.6 + - - +
23A PRO* 1.3 88.4 - - - +
25A LYS* 1.3 63.1 + - + +
27A LEU* 3.1 13.1 + - + +
28A ARG* 3.0 52.0 + - - +
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Residues in contact with LYS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLU 5.6 2.7 - - - -
21A GLY 2.9 22.5 + - - +
22A LEU* 3.3 21.9 - - - +
24A GLU* 1.3 75.8 - - + +
26A ARG* 1.3 63.3 + - - +
27A LEU 3.1 1.0 + - - -
28A ARG* 3.2 13.0 + - - +
29A GLY* 3.2 17.3 + - - -
72A TYR* 3.9 24.4 - - + +
74A SER* 5.2 10.9 + - - +
75A ASN* 5.8 3.0 + - - +
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Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ASP* 3.1 37.4 + - - -
18A MET* 3.7 16.8 - - - +
22A LEU* 3.0 17.6 + - - +
23A PRO* 3.1 21.7 + - - +
25A LYS* 1.3 76.2 - - - +
27A LEU* 1.3 52.7 + - - +
29A GLY* 3.5 1.1 + - - +
30A LYS* 2.8 51.8 + - - +
71A SER 3.8 17.2 - - - +
72A TYR* 3.2 34.7 + - + +
206A 147 3.1 37.3 + - - -
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PRO 3.1 9.8 + - - +
24A GLU* 3.1 12.0 + - - +
26A ARG* 1.3 73.6 - - - +
28A ARG* 1.3 81.8 + - - +
29A GLY 3.1 1.1 - - - -
30A LYS* 3.7 3.8 - - + +
31A THR* 2.7 38.5 + - - +
41C PRO* 3.5 35.2 - - + +
42C SER* 4.6 10.3 - - - -
44C VAL* 5.4 4.7 - - + -
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Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLU* 3.0 61.7 + - - +
25A LYS* 3.8 11.2 - - - +
27A LEU* 1.3 97.3 - - - +
29A GLY* 1.3 62.4 + - - +
31A THR* 3.2 8.0 - - - -
32A LEU* 3.2 32.2 + - + +
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Residues in contact with GLY 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS 3.2 8.1 + - - -
26A ARG 3.8 2.7 - - - -
27A LEU 3.1 0.6 - - - -
28A ARG* 1.3 76.2 - - - +
30A LYS* 1.3 60.2 + - - +
31A THR 3.0 1.8 - - - -
32A LEU* 3.4 8.9 + - - +
33A MET* 3.0 28.9 + - - +
54A MET* 6.0 0.9 - - - -
70A PHE* 3.4 12.9 - - - -
72A TYR 3.6 22.0 - - - -
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Residues in contact with LYS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ARG* 2.8 40.2 + - - +
27A LEU* 3.9 5.4 - - + +
29A GLY* 1.3 74.4 - - - +
31A THR* 1.3 57.5 + - - +
33A MET* 3.6 23.1 - - + +
34A TYR* 3.0 21.8 + - - +
70A PHE* 3.4 22.9 + - + +
71A SER* 3.3 30.8 + - - +
206A 147 5.1 3.0 + - - -
41C PRO* 3.4 26.5 - - + +
47C ARG* 6.0 2.0 - - - +
65C GLU* 3.8 27.8 + - - +
85C ASN* 5.6 0.4 + - - -
86C PHE* 3.8 12.3 - - + -
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Residues in contact with THR 31 (chain A).
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* 2.7 25.3 + - - +
28A ARG* 3.2 14.1 - - - -
30A LYS* 1.3 75.7 - - - +
32A LEU* 1.3 70.3 + - + +
34A TYR* 3.2 5.0 + - - +
35A GLU* 3.1 36.5 + - - +
40C HIS* 4.3 18.4 - - + -
41C PRO* 4.1 15.7 - - - +
42C SER* 6.1 0.5 - - - -
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 3.2 21.8 + - + +
29A GLY* 4.0 6.3 - - - +
31A THR* 1.3 79.4 - - + +
33A MET* 1.3 63.6 + - - +
35A GLU* 3.3 16.0 + - - +
36A PHE* 2.9 23.0 + - - +
50A LEU* 3.9 23.3 - - + +
53A GLU* 4.2 28.7 - - + +
54A MET* 4.0 33.5 - - + +
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Residues in contact with MET 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLY 3.0 17.6 + - - +
30A LYS* 3.6 21.8 - - + +
32A LEU* 1.3 77.8 - - - +
34A TYR* 1.3 57.7 + - + +
36A PHE* 3.2 7.6 + - - +
37A ASN* 3.0 31.8 + - - +
54A MET* 4.5 1.6 - - - -
68A VAL* 3.6 22.0 - - - +
69A TYR* 3.7 27.6 - - + -
70A PHE* 3.5 45.9 - - + +
65C GLU* 5.7 0.2 - - - +
66C PRO 5.0 3.8 - - - +
86C PHE* 4.1 13.2 - - + -
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Residues in contact with TYR 34 (chain A).
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 3.0 18.8 + - - +
31A THR 3.2 5.6 + - - +
33A MET* 1.3 77.9 - - + +
35A GLU* 1.3 74.4 + - + +
37A ASN* 3.4 2.4 + - - +
38A HIS* 3.1 74.7 + + + +
37C ASN 5.7 0.2 - - - -
38C HIS 3.7 23.2 + - - -
39C SER 4.0 9.4 - - - -
40C HIS* 3.1 39.5 + + - +
41C PRO* 3.9 16.6 - - + -
47C ARG* 5.9 0.4 - - - -
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Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A THR* 3.1 28.7 + - - +
32A LEU* 3.5 22.4 - - - +
34A TYR* 1.3 86.6 - - + +
36A PHE* 1.3 63.0 + - - +
38A HIS* 4.0 2.4 - - - -
39A SER* 3.2 23.7 + - - -
46A LYS* 3.5 25.0 + - - +
50A LEU* 4.1 15.8 - - + +
40C HIS* 4.6 8.1 + - - -
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Residues in contact with PHE 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU 2.9 14.3 + - - +
33A MET* 3.3 9.2 - - - +
35A GLU* 1.3 76.3 - - - +
37A ASN* 1.3 78.7 + - - +
39A SER* 2.7 24.6 + - - -
47A ARG* 3.5 35.7 - - + -
50A LEU* 3.8 24.0 - - + +
51A ILE* 3.8 11.0 - - + -
54A MET* 3.7 22.4 - - + -
64A VAL* 3.3 31.9 - - + -
66A PRO* 3.5 28.3 - - + +
68A VAL* 3.6 21.1 - - + -
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Residues in contact with ASN 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A MET* 3.0 21.8 + - - +
34A TYR* 4.2 4.0 - - - +
36A PHE* 1.3 92.1 - - - +
38A HIS* 1.3 69.9 + - + +
39A SER 3.3 4.0 + - - +
47A ARG* 5.6 0.3 + - - -
66A PRO* 3.9 10.4 - - - +
67A PRO* 3.3 27.3 - - + +
68A VAL* 3.0 38.8 - - - +
69A TYR* 3.9 10.9 - - - -
34B TYR* 5.6 0.5 - - - -
38B HIS* 4.4 9.7 - - - -
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Residues in contact with HIS 38 (chain A).
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* 3.1 65.1 + + + +
35A GLU* 4.0 2.0 - - - +
37A ASN* 1.3 84.1 - - + +
39A SER* 1.3 63.3 + - - +
40A HIS 3.6 0.2 + - - -
34B TYR* 3.4 21.8 + - - -
38B HIS* 3.1 34.8 + + + -
37C ASN 4.3 12.0 + - - -
38C HIS* 3.5 23.3 + + - -
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Residues in contact with SER 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU 3.2 18.1 + - - -
36A PHE* 2.7 18.4 + - - -
37A ASN 3.3 3.2 - - - +
38A HIS* 1.3 80.0 - - - +
40A HIS* 1.3 61.7 + - - +
41A PRO* 3.7 0.7 - - - +
43A GLU* 4.1 8.3 - - - -
46A LYS* 4.0 23.1 - - - +
47A ARG* 3.1 37.8 + - - +
34B TYR* 4.0 6.8 - - - -
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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