Contacts of the helix formed by residues 4 - 18 (chain G) 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 SER 4 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3G GLN* 1.3 75.7 - - - +
5G PHE* 1.3 61.1 + - - +
6G THR* 3.9 5.1 - - - -
7G SER* 3.1 25.7 + - - -
8G ILE* 3.0 29.0 + - - +
111G GLU* 3.5 19.5 - - - -
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Residues in contact with PHE 5 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C VAL* 3.3 45.3 - - + -
379C TYR* 6.2 1.8 - + - -
382C ARG* 6.2 0.4 - - - -
3G GLN 4.9 1.1 - - - -
4G SER* 1.3 69.4 - - - +
6G THR* 1.3 58.5 + - - +
7G SER 3.0 1.3 - - - -
8G ILE* 3.6 18.4 - - + +
9G ALA* 2.7 37.2 + - - +
45G PHE* 5.0 6.5 - + - -
46G ASP* 5.7 0.4 - - - -
49G ILE* 3.6 36.1 - - + -
55G ILE* 6.1 0.2 - - + -
56G MET* 5.5 3.1 - - + -
104G LEU* 4.0 20.0 - - + -
107G ILE* 3.5 26.0 - - + -
108G LEU* 3.6 14.8 - - + -
111G GLU* 2.9 21.3 + - - +
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Residues in contact with THR 6 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G SER* 3.2 4.9 - - - +
5G PHE* 1.3 79.1 - - - +
7G SER* 1.3 56.3 + - - +
9G ALA* 3.9 2.1 - - - +
10G ARG* 3.0 27.5 + - + +
108G LEU* 3.6 17.4 + - - +
111G GLU* 2.8 33.3 + - - +
112G ALA* 4.6 5.6 + - + +
115G LYS* 6.2 3.6 - - - -
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Residues in contact with SER 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G GLN* 3.4 19.7 + - - +
4G SER* 3.1 24.8 + - - -
5G PHE 3.0 0.2 - - - -
6G THR* 1.3 77.7 - - - +
8G ILE* 1.3 65.8 + - - +
10G ARG* 3.0 26.1 + - - +
11G ILE* 3.2 18.4 + - - +
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Residues in contact with ILE 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C VAL* 4.4 14.1 - - + -
375C ASN* 3.6 45.3 - - + +
376C VAL* 4.3 5.5 - - - +
379C TYR* 3.6 30.9 - - + -
3G GLN* 3.4 19.7 - - - +
4G SER 3.0 15.6 + - - +
5G PHE* 3.3 27.8 + - + +
7G SER* 1.3 74.8 - - - +
9G ALA* 1.3 58.3 + - - +
11G ILE* 3.5 4.4 + - - +
12G GLY* 2.9 27.7 + - - -
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Residues in contact with ALA 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C TYR* 3.6 31.2 - - + +
385C LYS* 5.1 2.0 - - - +
5G PHE 2.7 23.0 + - - +
6G THR* 4.1 2.7 - - - +
8G ILE* 1.3 70.5 - - - +
10G ARG* 1.3 66.4 + - - +
12G GLY 4.0 0.2 - - - -
13G ASP* 3.0 30.6 + - - +
104G LEU* 5.4 1.6 - - + -
108G LEU* 4.3 20.2 - - + -
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Residues in contact with ARG 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G THR* 3.0 15.3 + - + +
7G SER* 3.0 17.1 + - - +
9G ALA* 1.3 80.0 - - - +
11G ILE* 1.3 72.8 + - - +
12G GLY 3.2 0.2 + - - -
13G ASP* 3.3 8.2 + - - +
14G TYR* 3.3 13.4 + - + +
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Residues in contact with ILE 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C THR* 4.9 9.6 - - + -
376C VAL* 4.0 23.8 - - + -
3G GLN* 4.6 9.0 - - - +
7G SER* 3.2 21.4 + - - +
8G ILE* 3.9 5.2 - - - +
10G ARG* 1.3 89.9 - - + +
12G GLY* 1.3 64.4 + - - +
14G TYR* 3.4 8.4 + - + +
15G ILE* 3.2 41.1 + - + +
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Residues in contact with GLY 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376C VAL* 3.9 6.5 - - - +
379C TYR* 3.7 10.1 - - - -
380C ILE* 3.5 25.4 - - - +
8G ILE 2.9 17.2 + - - -
11G ILE* 1.3 77.9 - - - +
13G ASP* 1.3 56.1 + - - +
15G ILE* 3.2 6.3 + - - +
16G LEU* 2.9 28.2 + - - +
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Residues in contact with ASP 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C TYR* 2.9 25.6 + - - -
383C VAL* 4.3 0.3 - - - +
385C LYS* 3.7 27.9 + - - +
9G ALA* 3.0 21.4 + - - +
10G ARG* 3.3 4.2 + - - +
12G GLY* 1.3 71.2 - - - +
14G TYR* 1.3 56.0 + - - +
16G LEU* 3.0 15.0 + - - +
17G LYS* 2.8 59.4 + - - +
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Residues in contact with TYR 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ARG* 3.3 10.1 + - + +
11G ILE* 3.5 11.4 - - + +
13G ASP* 1.3 77.9 - - - +
15G ILE* 1.3 73.5 + - + +
17G LYS* 3.4 10.2 + - + +
18G SER* 3.3 25.3 + - - -
21G LEU* 4.4 21.7 - - + +
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Residues in contact with ILE 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C VAL* 3.8 25.8 - - + -
380C ILE* 4.5 13.0 - - + -
11G ILE* 3.2 26.0 - - + +
12G GLY* 3.3 5.6 - - - +
13G ASP 3.1 0.2 - - - -
14G TYR* 1.3 85.8 - - + +
16G LEU* 1.3 60.8 + - + +
17G LYS 2.9 6.8 + - - -
18G SER 3.3 19.1 - - - +
21G LEU* 3.7 36.7 - - + +
22G SER* 3.5 6.4 + - - +
25G CYS* 4.1 19.7 - - + -
26G VAL* 5.9 0.4 - - + +
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Residues in contact with LEU 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379C TYR* 4.6 1.3 - - + -
380C ILE* 4.0 24.0 - - + +
383C VAL* 3.3 45.3 - - + +
384C ASN* 5.7 0.4 - - - -
385C LYS* 5.1 6.3 - - + +
12G GLY 2.9 13.5 + - - +
13G ASP* 3.4 17.7 - - - +
15G ILE* 1.3 77.1 - - + +
17G LYS* 1.3 60.2 + - + +
22G SER* 3.8 15.8 + - - +
26G VAL* 3.6 31.6 - - + -
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Residues in contact with LYS 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385C LYS* 6.0 4.9 - - - +
13G ASP* 2.8 40.7 + - - +
14G TYR* 3.8 8.5 - - + +
15G ILE 2.9 2.8 + - - -
16G LEU* 1.3 77.9 - - + +
18G SER* 1.3 59.5 + - - +
19G PRO* 2.9 17.7 - - - +
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Residues in contact with SER 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G TYR* 3.3 16.8 + - - -
15G ILE 3.3 2.8 - - - +
17G LYS* 1.3 77.6 - - - +
19G PRO* 1.4 56.9 - - - +
20G VAL* 2.8 27.5 + - - +
21G LEU* 2.9 38.5 + - - +
22G SER* 3.0 9.6 + - - -
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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