Contacts of the helix formed by residues 7 - 18 (chain C) in PDB entry 1KYO
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 ASN 7 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C PHE* 2.8 49.0 + - + +
5C LYS 3.6 0.2 - - - -
6C SER* 1.3 75.2 + - - +
8C VAL* 1.3 67.2 + - - +
9C TYR* 2.6 39.8 - - - +
10C LEU* 2.6 33.5 - - + +
11C SER* 3.0 25.1 + - - -
5S SER* 5.3 0.7 + - - -
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Residues in contact with VAL 8 (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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6C SER 3.7 2.7 + - - -
7C ASN* 1.3 80.4 - - - +
9C TYR* 1.3 103.6 + - + +
11C SER* 3.3 11.6 + - - -
12C LEU* 4.1 2.8 + - - +
112N THR* 5.0 7.6 - - + +
199N MET* 4.1 46.6 - - + +
200N ALA* 5.2 4.0 - - + -
203N ILE* 4.2 27.4 - - + -
5S SER* 5.8 2.7 - - - -
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Residues in contact with TYR 9 (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 ASN* 2.6 15.1 - - - +
8C VAL* 1.3 96.0 - - + +
10C LEU* 1.3 67.1 + - + +
11C SER 3.1 1.3 - - - -
12C LEU* 2.9 23.1 + - - +
13C VAL* 3.7 7.2 + - - +
112N THR* 4.1 12.6 - - - -
116N VAL* 3.7 13.4 - - + +
196N MET* 2.6 74.6 + - + +
199N MET* 4.1 23.3 - - + -
200N ALA* 3.3 13.5 - - - +
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Residues in contact with LEU 10 (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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3C PHE* 3.5 39.0 - - + -
4C ARG* 3.5 22.8 - - + +
7C ASN* 2.6 20.8 - - + +
9C TYR* 1.3 74.3 - - + +
11C SER* 1.3 56.9 + - - +
13C VAL* 3.0 19.4 + - + +
14C ASN* 2.8 24.4 + - - +
18C ILE* 5.8 0.2 - - - +
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Residues in contact with SER 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ARG 3.0 12.2 + - - -
5C LYS* 3.4 22.2 - - - -
6C SER 5.0 0.2 - - - -
7C ASN 3.0 21.8 + - - -
8C VAL* 3.3 8.3 + - - -
9C TYR 3.0 1.8 + - - -
10C LEU* 1.3 74.0 - - - +
12C LEU* 1.3 72.6 + - - +
14C ASN* 3.6 3.4 - - - +
15C SER* 3.0 26.3 + - - -
3S PRO* 5.5 2.9 - - - +
4S PRO 5.6 1.6 - - - -
5S SER* 5.0 6.4 + - - -
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Residues in contact with LEU 12 (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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8C VAL 4.1 1.3 + - - +
9C TYR 2.9 13.4 + - - +
11C SER* 1.3 84.7 + - - +
13C VAL* 1.3 63.5 + - + +
15C SER* 3.2 7.0 + - - +
16C TYR* 3.0 50.6 + - + +
199N MET* 4.2 25.6 - - + -
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Residues in contact with VAL 13 (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 TYR 4.1 9.4 - - - +
10C LEU* 3.2 21.5 - - + +
12C LEU* 1.3 77.7 - - + +
14C ASN* 1.3 66.8 + - - +
16C TYR* 2.9 4.7 + - - -
17C ILE* 2.8 50.5 + - + +
18C ILE* 4.4 13.5 - - + -
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Residues in contact with ASN 14 (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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4C ARG* 2.5 57.1 - - + +
5C LYS* 3.9 14.3 - - - +
10C LEU 2.8 15.2 + - - +
11C SER* 3.2 7.7 + - - +
13C VAL* 1.3 72.5 - - - +
15C SER* 1.3 59.9 + - - +
18C ILE* 3.1 19.4 + - + +
19C ASP* 2.6 60.6 + - - +
12H TRP* 5.1 1.9 - - - -
3S PRO* 5.1 4.9 - - - +
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Residues in contact with SER 15 (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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11C SER 3.0 16.5 + - - -
12C LEU* 3.2 12.5 + - - +
14C ASN* 1.3 76.0 - - - +
16C TYR* 1.3 62.7 + - - +
20C SER* 3.7 5.0 - - - -
202C HIS* 2.7 35.4 + - - -
12H TRP* 3.4 29.3 - - - -
3S PRO* 3.8 24.2 - - - -
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Residues in contact with TYR 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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12C LEU* 3.0 46.2 + - + +
13C VAL* 2.9 3.2 + - - +
15C SER* 1.3 89.9 - - - +
17C ILE* 1.3 71.8 + - + +
18C ILE 3.9 0.2 - - - -
20C SER* 3.9 8.4 + - - -
198C LEU* 4.0 31.9 - - + -
199C MET* 4.0 18.2 - - + +
202C HIS* 3.6 47.8 - + + +
221C MET* 3.5 20.1 - - - +
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Residues in contact with ILE 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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13C VAL* 2.8 34.0 + - + +
16C TYR* 1.3 89.9 - - + +
18C ILE* 1.3 63.9 + - + +
221C MET* 3.0 25.3 - - - +
222C HIS* 3.7 6.1 + - - +
226C ILE* 3.6 27.0 - - + +
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Residues in contact with ILE 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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446A ARG* 3.1 20.1 + - - +
4C ARG* 4.1 17.9 - - + +
13C VAL* 4.3 13.0 - - + +
14C ASN* 3.1 30.2 + - + +
16C TYR 3.9 0.2 - - - -
17C ILE* 1.3 90.2 - - + +
19C ASP* 1.3 76.3 + - - +
20C SER 3.4 1.1 - - - -
220C PRO* 3.6 0.3 - - - +
221C MET 3.6 1.7 + - - -
222C HIS* 3.0 41.4 + - + +
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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