Contacts of the helix formed by residues 15 - 27 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C TYR* 1.3 79.1 - - + +
16C GLY* 1.3 65.0 + - - +
17C GLY 3.4 0.4 + - - -
18C PRO* 3.6 1.2 - - - +
19C THR* 2.8 34.0 + - - +
88C SER* 4.0 1.6 - - - +
129C LYS* 3.7 29.4 - - + +
130C SER* 3.9 7.6 - - - +
161C GLN* 3.7 40.4 - - + +
163C LEU* 4.2 7.4 - - + -
502C UPG 2.9 47.2 + - - +
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Residues in contact with GLY 16 (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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9C CYS* 3.9 8.5 - - - -
11C GLY 3.5 16.4 - - - -
13C GLY 3.7 4.6 + - - +
15C VAL* 1.3 79.7 - - - +
17C GLY* 1.3 57.7 + - - +
19C THR* 4.8 2.0 - - - -
20C CYS* 3.0 35.3 + - - +
34C VAL* 4.6 1.6 - - - +
88C SER* 3.1 20.3 + - - -
129C LYS* 4.9 1.8 - - - -
502C UPG 4.2 0.8 + - - -
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Residues in contact with GLY 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ALA 4.3 1.5 - - - -
13C GLY 3.3 9.1 + - - +
16C GLY* 1.3 73.7 - - - +
18C PRO* 1.3 65.0 - - - +
20C CYS* 3.9 0.9 - - - +
21C SER* 2.6 40.0 + - - -
34C VAL* 4.7 11.4 - - - +
45C TRP* 3.8 23.8 - - - -
71C PHE* 4.7 2.9 - - - -
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Residues in contact with PRO 18 (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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13C GLY 3.4 7.2 - - - +
14C TYR* 3.2 28.5 - - - +
15C VAL 3.6 2.0 - - - +
17C GLY* 1.3 89.4 - - - +
19C THR* 1.3 61.9 + - - +
21C SER* 3.3 1.4 + - - -
22C VAL* 3.0 29.1 + - - +
45C TRP* 4.0 6.0 - - + -
52C ILE* 4.8 7.2 - - + -
54C GLU* 5.4 2.0 - - + -
57C LEU* 4.1 33.2 - - + -
163C LEU* 4.8 4.7 - - + -
168C ALA* 4.8 11.2 - - + -
169C ILE* 4.9 2.9 - - + +
172C LEU* 3.7 14.1 - - + -
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Residues in contact with THR 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C VAL* 2.8 32.5 + - - +
16C GLY 4.2 0.2 - - - -
18C PRO* 1.3 78.5 - - - +
20C CYS* 1.3 62.6 + - - +
22C VAL* 3.3 2.9 + - - +
23C ILE* 3.1 33.3 + - + +
129C LYS* 3.4 33.3 - - - -
161C GLN* 5.1 2.1 - - - +
163C LEU* 4.0 6.9 - - - +
172C LEU* 3.7 29.0 - - + +
199C TYR* 4.6 8.1 - - + +
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Residues in contact with CYS 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 4.6 1.1 - - - -
9C CYS* 3.3 33.2 - - - -
16C GLY 3.0 16.1 + - - +
19C THR* 1.3 77.9 - - - +
21C SER* 1.3 64.2 + - - +
23C ILE* 3.7 8.3 - - - +
24C ALA* 3.0 24.1 + - - +
32C VAL* 3.7 18.3 - - + +
34C VAL* 3.7 19.1 - - + -
69C LEU* 4.2 2.0 - - - +
86C PHE* 3.8 26.2 - - - -
129C LYS* 5.2 1.6 - - - -
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Residues in contact with SER 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLY 2.6 26.3 + - - -
18C PRO* 3.6 7.4 - - - -
20C CYS* 1.3 77.5 - - - +
22C VAL* 1.3 61.8 + - - +
24C ALA* 3.4 3.6 + - - +
25C HIS* 3.0 23.4 + - - +
45C TRP* 4.6 0.3 - - - -
57C LEU* 4.4 2.2 - - - -
60C VAL* 3.7 12.4 - - - +
61C VAL* 3.6 26.1 - - - +
64C CYS* 4.0 2.4 - - - -
69C LEU* 3.7 23.0 - - - +
71C PHE* 3.8 8.3 - - - -
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Residues in contact with VAL 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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18C PRO 3.0 20.9 + - - +
19C THR 3.8 4.0 - - - +
21C SER* 1.3 73.9 - - - +
23C ILE* 1.3 65.2 + - - +
25C HIS* 3.1 3.5 + - + +
26C MET* 2.9 37.4 + - + +
60C VAL* 4.2 12.3 - - + -
169C ILE* 3.8 25.8 - - + -
172C LEU* 3.9 28.5 - - + -
173C LYS* 4.4 19.3 - - + -
202C TRP* 4.2 15.7 - - + -
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Residues in contact with ILE 23 (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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7C ILE* 4.0 17.7 - - + -
19C THR* 3.1 30.9 + - + +
20C CYS* 3.7 13.5 - - - +
21C SER 3.3 0.2 - - - -
22C VAL* 1.3 75.9 - - - +
24C ALA* 1.3 57.9 + - - +
26C MET 3.1 1.9 + - - -
27C CYS* 2.8 37.2 + - + +
30C ILE* 5.2 0.9 - - + -
32C VAL* 4.5 7.0 - - + -
86C PHE* 3.7 34.1 - - + -
198C VAL* 3.9 26.0 - - + -
199C TYR* 4.9 7.6 - - + +
202C TRP* 3.9 24.0 - - + -
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Residues in contact with ALA 24 (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 CYS 3.0 17.4 + - - +
21C SER 3.6 4.3 - - - +
22C VAL 3.3 0.2 - - - -
23C ILE* 1.3 75.7 - - - +
25C HIS* 1.3 62.9 + - - +
27C CYS 3.3 11.3 + - - -
28C PRO* 3.7 1.7 - - - +
32C VAL* 3.8 16.6 - - + +
64C CYS* 3.9 5.8 - - - +
68C ASN* 2.9 33.1 + - - +
69C LEU* 3.8 28.0 - - + -
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Residues in contact with HIS 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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21C SER 3.0 14.1 + - - +
22C VAL* 3.1 9.2 + - - +
24C ALA* 1.3 77.7 - - - +
26C MET* 1.3 86.1 + - + +
28C PRO* 4.6 7.4 - - - +
60C VAL* 3.9 19.0 + - + +
63C SER* 2.9 30.9 + - - -
64C CYS* 3.7 11.1 - - - +
173C LYS* 4.3 19.6 + - - -
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Residues in contact with MET 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C VAL* 2.9 22.5 + - + +
23C ILE 3.9 1.8 - - - +
25C HIS* 1.3 90.5 - - + +
27C CYS* 1.3 58.2 + - - +
28C PRO* 3.6 9.3 - - - +
173C LYS* 3.6 46.0 - - + -
201C HIS* 3.8 17.8 - - - +
202C TRP* 3.5 56.1 - - + -
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Residues in contact with CYS 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ILE* 2.8 18.0 + - + +
24C ALA* 3.4 3.4 - - - +
26C MET* 1.3 81.3 - - - +
28C PRO* 1.3 66.6 - - - +
29C GLU* 3.1 9.2 - - - +
30C ILE* 3.0 35.3 + - + +
68C ASN* 3.0 10.4 + - - -
198C VAL* 3.7 23.3 - - - -
201C HIS* 3.5 31.9 - - + -
202C TRP* 4.1 10.3 - - - -
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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