Contacts of the helix formed by residues 16 - 32 (chain C) in PDB entry 1KBO
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 SER 16 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C HIS* 3.5 29.4 + - - -
13C GLU* 2.9 19.6 + - - -
14C ARG 4.8 0.5 - - - +
15C THR* 1.3 82.2 + - - +
17C PHE* 1.3 59.6 + - - +
18C ASN 3.5 1.2 + - - -
19C TYR* 3.2 16.8 + - - +
20C ALA* 2.9 24.3 + - - +
603C FAD 3.3 29.0 + - - -
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Residues in contact with PHE 17 (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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16C SER* 1.3 71.3 - - - +
18C ASN* 1.3 55.5 + - - +
20C ALA* 3.0 6.4 + - + +
21C MET* 2.5 66.9 + - + +
147C THR* 4.4 9.0 - - + -
189C THR* 4.1 6.1 - - + -
192C ILE* 3.5 30.5 - - + -
200C ARG* 3.7 19.7 - - + -
203C ILE* 3.6 32.5 - - + -
204C LEU* 3.4 30.1 - - + -
603C FAD 3.0 56.4 + + - +
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Residues in contact with ASN 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 4.1 4.7 - - + +
11C HIS* 3.8 14.6 - - + -
16C SER* 3.7 6.7 - - - +
17C PHE* 1.3 77.7 - - - +
19C TYR* 1.3 56.2 + - - +
21C MET* 3.1 9.4 + - - +
22C LYS* 2.8 25.5 + - - +
100C GLN* 2.7 33.0 + - - +
101C PHE* 3.1 22.7 + - - +
102C PRO* 3.4 20.7 - - - +
147C THR* 3.1 28.2 + - - +
603C FAD 3.0 23.5 + - - +
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Residues in contact with TYR 19 (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 LEU* 3.7 17.4 - - + +
11C HIS* 5.8 2.5 - - + -
13C GLU 3.6 17.5 - - - +
14C ARG* 3.4 57.5 - - + +
16C SER* 3.2 12.1 + - - +
18C ASN* 1.3 77.4 - - - +
20C ALA* 1.3 64.7 + - - +
22C LYS* 3.0 34.5 + - - +
23C GLU* 2.9 52.0 + - + +
40C ASP* 3.8 16.3 + - - -
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Residues in contact with ALA 20 (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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16C SER 2.9 14.5 + - - +
17C PHE* 3.1 14.8 - - + +
19C TYR* 1.3 78.2 - - - +
21C MET* 1.3 56.7 + - - +
23C GLU* 3.1 7.7 + - - +
24C ALA* 2.9 29.8 + - - +
204C LEU* 4.1 14.8 - - + +
603C FAD 3.4 33.0 - - + +
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Residues in contact with MET 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PHE* 2.5 59.2 + - + +
18C ASN* 3.2 10.3 - - - +
20C ALA* 1.3 73.7 - - - +
22C LYS* 1.3 59.2 + - - +
24C ALA* 3.5 2.5 + - - +
25C ALA* 3.2 16.6 + - - +
100C GLN* 3.2 25.1 - - - +
145C SER* 3.0 29.2 - - - +
146C ILE 5.1 1.1 - - - +
147C THR* 5.0 1.8 - - + -
187C GLN* 4.6 5.2 - - + -
189C THR* 3.9 20.0 - - - +
203C ILE* 4.4 8.5 - - + -
204C LEU* 4.1 9.0 - - - -
207C TRP* 3.4 37.6 + - + -
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Residues in contact with LYS 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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7C ILE* 3.9 24.9 - - + +
9C LEU* 3.4 29.1 - - + +
18C ASN 2.8 12.7 + - - +
19C TYR* 3.0 42.5 + - - +
21C MET* 1.3 74.3 - - - +
23C GLU* 1.3 90.4 + - - +
25C ALA* 3.2 6.9 + - - +
26C ALA* 2.9 26.3 + - - +
38C GLU* 3.3 38.7 + - + +
40C ASP* 4.6 2.9 + - + +
100C GLN* 4.3 9.4 + - + -
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Residues in contact with GLU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR* 2.9 42.5 + - + +
20C ALA* 3.6 9.2 - - - +
22C LYS* 1.3 99.5 + - - +
24C ALA* 1.3 60.2 + - - +
26C ALA* 3.7 12.7 - - - +
27C ALA* 3.0 29.5 + - - +
38C GLU* 4.2 2.6 - - - +
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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 ALA 2.9 14.3 + - - +
21C MET* 3.5 11.0 - - - +
23C GLU* 1.3 77.7 - - - +
25C ALA* 1.3 57.7 + - - +
27C ALA 3.4 0.9 + - - -
28C ALA* 2.9 26.3 + - - +
204C LEU* 4.2 18.8 - - + +
207C TRP* 4.3 5.6 - - + -
208C LYS* 3.0 39.4 - - + +
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Residues in contact with ALA 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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7C ILE* 4.1 10.5 - - + -
21C MET 3.2 9.2 + - - +
22C LYS* 3.2 9.8 + - - +
24C ALA* 1.3 78.3 - - - +
26C ALA* 1.3 66.3 + - - +
29C LEU* 2.9 30.1 + - - +
98C ILE* 4.1 20.4 - - + -
207C TRP* 3.9 8.3 - - + +
211C LEU* 3.3 26.7 - - + +
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Residues in contact with ALA 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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7C ILE* 4.0 14.9 - - + +
22C LYS 2.9 16.4 + - - +
23C GLU* 3.7 18.6 - - - +
25C ALA* 1.3 75.8 - - - +
27C ALA* 1.3 63.6 + - - +
30C LYS* 3.0 47.1 + - - +
36C VAL* 4.0 11.0 - - + +
38C GLU* 4.8 7.9 - - - +
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Residues in contact with ALA 27 (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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23C GLU 3.0 19.1 + - - +
26C ALA* 1.3 77.7 - - - +
28C ALA* 1.3 66.1 + - - +
30C LYS* 3.6 8.7 - - - +
31C LYS* 3.0 26.4 + - + +
208C LYS* 3.4 20.4 - - - +
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Residues in contact with ALA 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 ALA 2.9 17.3 + - - +
25C ALA 3.8 2.2 - - - +
27C ALA* 1.3 74.9 - - - +
29C LEU* 1.3 56.6 + - - +
31C LYS* 2.7 46.2 + - - +
32C LYS* 3.3 8.2 + - - +
208C LYS* 3.7 31.8 - - + +
211C LEU* 4.0 16.6 - - + -
212C GLU* 5.8 3.4 - - + -
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Residues in contact with LEU 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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5C ALA* 4.1 18.8 - - + -
7C ILE* 4.5 5.2 - - + -
25C ALA* 2.9 22.1 + - + +
28C ALA* 1.3 74.8 - - - +
30C LYS* 1.3 53.5 + - - +
31C LYS 3.4 0.2 + - - -
32C LYS* 3.5 4.0 + - - +
34C TRP* 2.8 65.8 + - + +
36C VAL* 3.7 17.3 - - + -
96C LEU* 4.6 7.0 - - + -
98C ILE* 3.8 26.7 - - + -
211C LEU* 3.6 42.4 - - + +
214C ILE* 4.9 0.4 - - + -
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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
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26C ALA* 3.0 38.5 + - - +
27C ALA* 3.6 7.2 - - - +
29C LEU* 1.3 73.6 - - - +
31C LYS* 1.3 67.0 + - - +
33C GLY* 3.0 14.4 + - - -
34C TRP 3.9 11.7 - - - +
36C VAL* 3.8 28.5 - - + +
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Residues in contact with LYS 31 (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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27C ALA* 3.0 12.5 + - + +
28C ALA* 2.7 35.5 + - - +
30C LYS* 1.3 68.0 - - - +
32C LYS* 1.3 55.7 + - + +
33C GLY* 2.7 15.6 + - - -
208C LYS* 3.1 37.2 - - - +
212C GLU* 6.4 3.6 - - - -
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Residues in contact with LYS 32 (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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28C ALA 3.3 9.2 + - - +
29C LEU* 3.5 5.8 + - - +
30C LYS 3.4 0.2 - - - -
31C LYS* 1.3 79.5 - - + +
33C GLY* 1.3 62.2 + - - +
34C TRP* 3.2 19.0 + - + +
211C LEU 5.2 1.3 - - - +
212C GLU* 3.1 64.6 + - + +
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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