Contacts of the helix formed by residues 15 - 27 (chain B) in PDB entry 3KHU
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 VAL 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B TYR* 1.3 79.6 - - + +
16B GLY* 1.3 66.0 + - - +
17B GLY 3.5 0.2 - - - -
18B PRO* 3.7 0.9 - - - +
19B THR* 2.7 31.3 + - - +
88B SER* 3.9 4.5 - - - +
129B LYS* 3.8 23.8 - - + +
130B SER* 3.9 4.3 - - - +
161B GLN* 3.7 35.0 - - + -
163B LEU* 4.2 10.6 - - + +
502B UPG 2.9 50.9 + - - +
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Residues in contact with GLY 16 (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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9B CYS* 3.8 8.7 - - - -
11B GLY 3.5 16.8 + - - -
13B GLY 3.7 3.6 + - - +
15B VAL* 1.3 78.4 - - - +
17B GLY* 1.3 64.7 - - - +
19B THR* 4.8 2.2 - - - -
20B CYS* 3.0 29.8 + - - +
34B VAL* 4.7 1.5 - - - +
88B SER* 3.2 20.1 + - - -
129B LYS* 4.9 1.8 - - - -
502B UPG 4.2 1.0 + - - -
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Residues in contact with GLY 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLY 4.3 0.2 + - - -
12B ALA 4.2 0.8 - - - -
13B GLY 3.3 9.5 + - - +
16B GLY* 1.3 74.8 - - - +
18B PRO* 1.3 61.6 - - - +
20B CYS* 4.3 0.3 - - - +
21B SER* 2.7 39.9 + - - -
34B VAL* 4.6 11.6 - - - +
45B TRP* 3.7 25.6 - - - -
71B PHE* 4.7 2.6 - - - -
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Residues in contact with PRO 18 (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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13B GLY 3.4 7.2 - - - +
14B TYR* 3.2 27.1 - - - +
15B VAL 3.7 2.9 - - - +
17B GLY* 1.3 90.6 - - - +
19B THR* 1.3 61.5 + - - +
21B SER* 3.3 1.4 + - - -
22B VAL* 3.0 29.8 + - - +
45B TRP* 4.0 5.8 - - + -
52B ILE* 4.8 7.6 - - + -
54B GLU* 5.4 1.8 - - + -
57B LEU* 4.0 33.0 - - + -
163B LEU* 4.7 4.5 - - + -
168B ALA* 4.8 13.2 - - + -
169B ILE* 4.9 2.9 - - + +
172B LEU* 3.7 15.0 - - + -
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Residues in contact with THR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL 2.7 23.6 + - - -
16B GLY 4.2 1.3 - - - -
18B PRO* 1.3 79.0 - - - +
20B CYS* 1.3 58.5 + - - +
22B VAL* 3.3 3.5 + - - +
23B ILE* 3.0 38.6 + - + +
129B LYS* 3.2 32.8 - - - -
161B GLN* 3.5 31.3 - - - +
163B LEU* 3.9 3.6 - - - +
172B LEU* 3.7 19.1 - - + +
199B TYR* 4.7 3.1 - - + +
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Residues in contact with CYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 4.7 1.3 - - - -
9B CYS* 3.3 37.7 - - - -
16B GLY 3.0 15.2 + - - +
19B THR* 1.3 77.3 - - - +
21B SER* 1.3 64.3 + - - +
23B ILE* 3.4 8.8 + - - +
24B ALA* 3.1 23.0 + - - +
32B VAL* 3.7 24.3 - - + +
34B VAL* 3.7 13.5 - - + -
69B LEU* 4.3 1.5 - - - +
86B PHE* 3.8 24.2 - - - -
129B LYS* 5.1 1.3 - - - -
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Residues in contact with SER 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLY 2.7 25.5 + - - -
18B PRO* 3.6 7.2 - - - -
20B CYS* 1.3 78.3 - - - +
22B VAL* 1.3 56.0 + - - +
24B ALA* 3.3 3.6 + - - +
25B HIS* 3.0 28.4 + - - +
45B TRP* 4.7 0.3 - - - -
57B LEU* 4.4 1.8 - - - -
60B VAL* 3.7 11.8 - - - +
61B VAL* 3.6 30.0 - - - +
64B CYS* 4.0 2.4 - - - -
69B LEU* 3.6 20.2 - - - +
71B PHE* 3.8 8.5 - - - -
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Residues in contact with VAL 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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18B PRO 3.0 20.4 + - - +
19B THR 3.7 4.0 - - - +
21B SER* 1.3 72.6 - - - +
23B ILE* 1.3 66.4 + - - +
25B HIS* 3.2 7.6 + - + +
26B MET* 3.0 36.7 + - + +
60B VAL* 4.2 7.9 - - + -
169B ILE* 3.8 26.7 - - + -
172B LEU* 3.8 27.6 - - + -
173B LYS* 4.4 18.6 - - + -
202B TRP* 4.2 15.5 - - + -
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Residues in contact with ILE 23 (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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7B ILE* 4.0 22.4 - - + -
19B THR* 3.0 31.1 + - + +
20B CYS* 3.6 13.7 - - - +
22B VAL* 1.3 75.5 - - - +
24B ALA* 1.3 58.0 + - - +
26B MET 3.1 2.3 + - - -
27B CYS* 2.8 36.2 + - + +
30B ILE* 5.3 0.7 - - + -
32B VAL* 4.2 7.9 - - + -
86B PHE* 3.7 35.0 - - + -
198B VAL* 4.0 20.4 - - + -
199B TYR* 4.8 8.1 - - + +
202B TRP* 3.9 22.7 - - + -
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Residues in contact with ALA 24 (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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20B CYS 3.1 14.9 + - - +
21B SER 3.6 7.2 - - - +
23B ILE* 1.3 75.7 - - - +
25B HIS* 1.3 62.1 + - - +
26B MET 3.3 0.5 + - - -
27B CYS 3.3 10.3 + - - -
28B PRO* 3.7 1.9 - - - +
32B VAL* 3.8 18.2 - - + -
64B CYS* 4.0 4.9 - - - +
68B ASN* 2.9 34.3 + - - +
69B LEU* 3.8 27.8 - - + -
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Residues in contact with HIS 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 SER 3.0 14.3 + - - +
22B VAL* 3.5 8.5 - - - +
24B ALA* 1.3 78.2 - - - +
26B MET* 1.3 85.4 + - + +
28B PRO* 4.7 7.1 - - - +
60B VAL* 3.9 19.9 + - + +
63B SER* 2.9 31.9 + - - -
64B CYS* 3.7 11.5 - - - +
173B LYS* 4.3 19.1 + - - -
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Residues in contact with MET 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL* 3.0 22.2 + - + +
23B ILE 3.9 1.6 - - - +
25B HIS* 1.3 93.3 - - + +
27B CYS* 1.3 61.0 + - - +
28B PRO* 3.5 8.9 - - - +
173B LYS* 3.6 46.2 - - + +
201B HIS* 3.8 15.1 - - - +
202B TRP* 3.5 55.4 - - + -
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Residues in contact with CYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 2.8 18.5 + - + +
24B ALA* 3.4 4.6 - - - +
26B MET* 1.3 83.2 - - - +
28B PRO* 1.4 66.4 - - - +
29B GLU* 3.1 9.0 - - - +
30B ILE* 3.0 35.0 + - + +
68B ASN* 3.0 10.4 + - - -
198B VAL* 3.7 22.0 - - - -
201B HIS* 3.7 28.3 - - + -
202B TRP* 4.0 11.7 - - - -
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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