Contacts of the helix formed by residues 21 - 38 (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 GLY 21 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B CYS* 3.1 1.8 - - - +
20B GLU* 1.3 78.6 - - - +
22B LEU* 1.3 64.6 + - - +
23B PRO* 3.1 4.3 - - - +
24B GLU* 3.0 27.4 + - - +
25B LYS* 2.8 28.7 + - - +
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Residues in contact with LEU 22 (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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5B MET* 5.0 5.2 - - + -
6B THR* 4.9 17.5 - - + -
9B ILE* 4.4 23.3 - - + -
16B THR 4.4 3.6 - - - +
17B ASP* 3.4 29.6 - - + +
19B CYS 3.1 12.5 + - - +
20B GLU* 3.2 7.7 + - + +
21B GLY* 1.3 75.4 - - - +
23B PRO* 1.3 71.1 - - + +
25B LYS* 3.2 20.3 + - - +
26B ARG* 3.0 40.4 + - - +
72B TYR* 3.7 18.1 - - + +
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Residues in contact with PRO 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ASP 3.7 4.7 - - - +
18B MET* 3.6 37.2 - - + +
19B CYS* 3.6 11.2 - - - +
21B GLY* 3.2 6.5 - - - +
22B LEU* 1.3 95.2 - - + +
24B GLU* 1.3 70.1 + - - +
26B ARG* 3.2 21.3 + - - +
27B LEU* 3.1 20.6 + - - +
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY* 3.0 27.2 + - - +
23B PRO* 1.3 85.7 - - - +
25B LYS* 1.3 62.8 + - + +
27B LEU* 2.9 11.7 + - - -
28B ARG* 2.8 53.3 + - - +
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Residues in contact with LYS 25 (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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21B GLY 2.8 20.4 + - - +
22B LEU* 3.2 24.6 + - - +
24B GLU* 1.3 72.6 - - - +
26B ARG* 1.3 63.5 + - - +
28B ARG* 3.2 13.0 + - - +
29B GLY* 3.0 19.6 + - - -
72B TYR* 3.9 21.3 - - + +
74B SER* 4.5 20.1 + - - +
75B ASN* 5.4 7.7 + - - +
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Residues in contact with ARG 26 (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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17B ASP* 2.9 36.1 + - - -
18B MET* 3.5 23.8 - - - +
22B LEU* 3.0 24.7 + - - +
23B PRO* 3.5 18.3 - - - +
25B LYS* 1.3 76.4 - - - +
27B LEU* 1.3 54.0 + - - +
30B LYS* 2.6 53.9 + - - +
71B SER 3.5 17.5 - - - +
72B TYR* 3.0 45.7 + - + +
204B 147 3.5 24.7 + - - -
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PRO* 4.1 31.4 - - + +
42A SER* 4.5 12.6 - - - +
44A VAL* 5.7 3.8 - - + -
23B PRO 3.1 12.4 + - - +
24B GLU* 2.9 10.2 + - - +
26B ARG* 1.3 78.9 - - - +
28B ARG* 1.3 76.2 + - - +
30B LYS* 3.9 3.4 - - + +
31B THR* 2.3 39.4 + - - +
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Residues in contact with ARG 28 (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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24B GLU* 2.8 71.7 + - - +
25B LYS* 3.6 11.7 - - - +
27B LEU* 1.3 96.1 - - - +
29B GLY* 1.3 64.6 + - - +
31B THR* 2.9 17.8 + - - -
32B LEU* 3.2 20.8 + - + +
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Residues in contact with GLY 29 (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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25B LYS 3.0 10.1 + - - -
26B ARG 3.7 1.8 - - - -
28B ARG* 1.3 79.1 - - - +
30B LYS* 1.3 60.9 + - - +
31B THR 3.0 1.0 + - - -
32B LEU* 3.2 11.1 + - - +
33B MET* 3.1 21.7 + - - +
54B MET* 6.0 1.1 - - - -
70B PHE* 3.8 11.4 - - - -
72B TYR 3.4 24.0 - - - -
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Residues in contact with LYS 30 (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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41A PRO* 3.2 28.2 - - + +
47A ARG* 6.0 2.0 - - - +
65A GLU* 3.9 28.7 + - - +
86A PHE* 4.2 7.5 - - + -
26B ARG* 2.6 37.9 + - - +
27B LEU* 4.0 5.2 - - - +
29B GLY* 1.3 71.4 - - - +
31B THR* 1.3 60.8 + - - +
33B MET* 3.9 22.6 - - + +
34B TYR* 3.2 13.7 + - - +
70B PHE* 3.6 16.9 + - + +
71B SER* 3.5 37.3 + - - +
204B 147 5.3 2.8 + - - -
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Residues in contact with THR 31 (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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40A HIS* 3.6 27.5 - - + +
41A PRO* 4.0 10.2 - - - +
27B LEU* 2.3 30.7 + - - +
28B ARG* 2.9 11.8 + - - -
30B LYS* 1.3 78.2 - - - +
32B LEU* 1.3 68.1 + - + +
34B TYR* 3.3 4.7 + - - +
35B GLU* 3.2 31.8 + - - +
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Residues in contact with LEU 32 (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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28B ARG* 3.2 16.0 + - + +
29B GLY* 3.8 7.4 - - - +
31B THR* 1.3 75.8 - - + +
33B MET* 1.3 66.4 + - - +
35B GLU* 3.2 16.9 + - - +
36B PHE* 2.9 23.6 + - - +
50B LEU* 4.2 23.4 - - + +
53B GLU* 3.5 44.9 - - + +
54B MET* 4.1 18.3 - - + +
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Residues in contact with MET 33 (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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65A GLU* 5.7 0.2 - - - +
66A PRO 5.2 2.9 - - - +
86A PHE* 3.9 14.6 - - + -
29B GLY 3.1 15.4 + - - +
30B LYS* 3.9 22.2 - - + +
31B THR 3.2 0.2 - - - -
32B LEU* 1.3 77.3 - - - +
34B TYR* 1.3 57.6 + - + +
36B PHE* 3.2 6.3 + - - +
37B ASN* 2.9 34.0 + - - +
54B MET* 4.4 3.4 - - - -
68B VAL* 3.7 13.9 - - + +
69B TYR* 3.6 30.7 - - + -
70B PHE* 3.6 51.6 - - + +
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Residues in contact with TYR 34 (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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37A ASN 5.6 0.7 - - - -
38A HIS 3.4 23.2 + - - -
39A SER 4.0 9.6 - - - -
40A HIS* 3.3 38.2 + + - +
41A PRO* 3.7 20.6 - - + -
47A ARG* 5.9 0.2 - - - -
30B LYS 3.2 17.0 + - - +
31B THR 3.5 4.7 - - - +
32B LEU 3.2 0.6 - - - -
33B MET* 1.3 84.6 - - + +
35B GLU* 1.3 70.8 + - + +
37B ASN* 4.6 3.1 - - - +
38B HIS* 3.0 72.5 + + + +
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Residues in contact with GLU 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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40A HIS* 4.1 15.6 + - - -
31B THR* 3.2 21.9 + - - +
32B LEU* 3.2 23.6 + - - +
34B TYR* 1.3 88.6 - - + +
36B PHE* 1.3 61.9 - - - +
38B HIS* 3.6 2.9 + - - +
39B SER* 3.2 22.9 + - - -
46B LYS* 3.8 23.7 + - - +
50B LEU* 4.0 12.3 - - + +
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Residues in contact with PHE 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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32B LEU 2.9 13.1 + - - +
33B MET* 3.5 8.7 - - - +
35B GLU* 1.3 76.4 - - - +
37B ASN* 1.3 78.0 + - - +
39B SER* 2.6 24.5 + - - +
47B ARG* 3.5 38.1 - - + -
50B LEU* 3.6 23.6 - - + -
51B ILE* 3.8 12.6 - - + -
54B MET* 3.5 29.4 - - + -
64B VAL* 3.4 28.5 - - + -
66B PRO* 3.7 29.7 - - + +
68B VAL* 4.0 10.3 - - + -
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Residues in contact with ASN 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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33B MET* 2.9 24.8 + - - +
34B TYR* 4.0 4.4 - - - +
36B PHE* 1.3 90.0 - - - +
38B HIS* 1.3 71.0 + - + +
39B SER 3.3 3.9 + - - +
66B PRO* 4.4 9.3 - - - +
67B PRO* 3.4 23.6 - - + +
68B VAL* 3.0 41.6 + - - +
69B TYR* 3.8 11.1 + - - -
34C TYR* 5.5 0.3 - - - -
38C HIS* 4.6 9.5 + - - -
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Residues in contact with HIS 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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37A ASN 4.4 11.0 + - - -
38A HIS* 3.1 37.5 + + + -
34B TYR* 3.0 67.6 + + + +
35B GLU* 3.9 3.4 - - - +
37B ASN* 1.3 84.4 - - + +
39B SER* 1.3 62.6 - - - +
40B HIS 3.6 0.5 + - - -
34C TYR* 3.5 22.2 + - - -
38C HIS* 3.6 17.6 + + - -
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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