Contacts of the helix formed by residues 31 - 52 (chain N) 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 31 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27N ASN 4.2 1.7 - - - +
28N TYR* 3.1 30.5 + - - +
29N TRP 3.1 0.8 - - - -
30N TRP* 1.3 79.6 - - - +
32N MET* 1.3 64.0 + - + +
33N GLY 3.2 2.9 - - - -
34N SER* 3.3 15.0 + - - -
35N LEU* 3.2 16.5 + - - +
225N PHE* 5.7 1.7 - - - -
228N LYS* 3.2 31.3 + - - +
229N ASP* 3.2 23.6 - - - +
232N THR* 2.9 42.6 + - + +
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Residues in contact with MET 32 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N TYR* 3.5 18.2 - - + +
29N TRP* 3.2 32.5 - - + +
30N TRP 3.3 0.6 - - - -
31N ASN* 1.3 78.9 - - + +
33N GLY* 1.3 64.6 + - - +
35N LEU* 3.3 24.9 + - + +
36N LEU* 3.0 27.2 + - - +
92N VAL* 3.7 12.0 - - + +
95N MET* 4.3 29.6 - - + +
96N HIS* 3.8 35.0 - - + +
99N LYS* 5.7 0.2 - - + -
232N THR* 5.0 5.2 - - + -
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Residues in contact with GLY 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30N TRP 4.0 0.2 + - - -
31N ASN 3.2 1.0 - - - -
32N MET* 1.3 76.0 - - - +
34N SER* 1.3 62.5 + - - +
36N LEU* 3.1 16.5 + - - +
37N GLY 3.2 8.5 + - - -
96N HIS* 3.8 4.2 + - - -
522N HEC 3.1 61.0 + - - +
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Residues in contact with SER 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30N TRP 4.8 2.2 + - - -
31N ASN* 3.3 13.3 + - - -
33N GLY* 1.3 70.5 - - - +
35N LEU* 1.3 65.4 + - - +
37N GLY* 2.9 5.8 + - - +
38N LEU* 2.9 20.6 + - - +
229N ASP* 2.8 38.5 + - - +
232N THR* 5.3 0.7 + - - -
233N VAL* 5.6 7.4 - - - -
522N HEC 4.3 6.2 - - - +
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Residues in contact with LEU 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31N ASN 3.2 21.5 + - - +
32N MET* 3.3 30.5 + - + +
33N GLY 3.2 0.4 - - - -
34N SER* 1.3 77.0 - - - +
36N LEU* 1.3 57.7 + - - +
38N LEU* 3.1 11.6 + - + +
39N CYS* 2.8 32.8 + - - -
92N VAL* 4.0 14.8 - - + -
232N THR* 3.8 39.0 - - - +
233N VAL* 3.9 22.7 - - + +
236N PHE* 4.0 25.7 - - + -
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Residues in contact with LEU 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N MET 3.0 16.9 + - - +
33N GLY 3.1 6.7 + - - +
35N LEU* 1.3 72.5 - - - +
37N GLY* 1.3 67.0 + - - +
39N CYS* 3.1 5.6 + - - +
40N LEU* 2.9 23.9 + - - +
89N PHE* 3.6 29.0 - - + +
92N VAL* 3.5 20.6 - - + -
93N MET* 3.7 19.3 - - + +
96N HIS* 3.5 28.0 - - + +
522N HEC 3.4 49.5 - - + +
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Residues in contact with GLY 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N GLY 3.2 6.5 + - - -
34N SER* 2.9 9.3 + - - -
36N LEU* 1.3 80.8 - - - +
38N LEU* 1.3 61.3 + - - +
40N LEU* 3.2 7.7 + - - +
41N VAL* 3.2 24.2 + - - +
194N VAL* 6.3 0.4 - - - -
522N HEC 4.0 10.7 - - - +
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Residues in contact with LEU 38 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N SER 2.9 10.5 + - - +
35N LEU* 3.2 14.4 - - + +
37N GLY* 1.3 76.2 - - - +
39N CYS* 1.3 59.5 + - - +
41N VAL* 3.0 13.2 + - + +
42N ILE* 2.8 46.4 + - + +
233N VAL* 3.4 39.9 - - + -
236N PHE* 4.4 20.9 - - + -
237N MET* 4.5 14.4 - - + -
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Residues in contact with CYS 39 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N LEU 2.8 21.4 + - - +
36N LEU* 3.1 9.6 + - - +
38N LEU* 1.3 75.6 - - - +
40N LEU* 1.3 63.2 + - - +
42N ILE* 3.1 8.8 + - - +
43N GLN* 2.9 30.4 + - - +
85N GLY 4.9 4.3 - - - +
88N PHE 4.7 0.7 - - - -
89N PHE* 3.9 41.7 - - + -
92N VAL* 5.1 3.8 - - - -
236N PHE* 3.6 32.8 - - - -
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Residues in contact with LEU 40 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36N LEU 2.9 11.7 + - - +
37N GLY* 3.2 12.3 + - - +
39N CYS* 1.3 76.3 - - - +
41N VAL* 1.3 57.7 + - + +
43N GLN* 3.5 1.5 + - - +
44N ILE* 3.0 48.0 + - + +
89N PHE* 3.9 13.4 - - + -
187N PRO* 4.9 1.8 - - + +
190N ILE* 3.8 25.6 - - + -
191N ALA* 3.9 32.8 - - + +
194N VAL* 4.5 13.7 - - + -
521N HEC 3.9 22.2 - - + -
522N HEC 5.1 3.8 - - + -
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Residues in contact with VAL 41 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37N GLY 3.2 13.4 + - - +
38N LEU* 3.0 15.3 + - + +
40N LEU* 1.3 75.6 - - + +
42N ILE* 1.3 69.5 + - + +
44N ILE* 3.1 6.6 + - + -
45N VAL* 2.8 42.3 + - + +
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Residues in contact with ILE 42 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N LEU* 2.8 42.2 + - + +
39N CYS* 3.7 8.1 - - - +
41N VAL* 1.3 71.4 - - + +
43N GLN* 1.3 73.8 + - - +
45N VAL* 4.9 2.0 - - - -
46N THR* 2.8 42.8 + - + +
81N LEU* 3.8 27.4 - - + +
85N GLY* 5.1 2.0 - - - -
236N PHE* 4.2 23.3 - - + -
237N MET* 5.0 9.6 - - + -
240N LEU* 4.4 11.9 - - + -
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Residues in contact with GLN 43 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39N CYS* 2.9 19.3 + - - +
40N LEU 3.8 1.6 - - - +
42N ILE* 1.3 86.0 - - - +
44N ILE* 1.3 58.3 + - - +
46N THR* 3.0 3.9 + - - -
47N GLY* 2.8 26.5 + - - -
81N LEU 4.1 1.6 + - - -
82N HIS* 2.9 39.1 + - - +
85N GLY* 3.3 34.6 + - - -
86N ALA* 3.5 8.5 + - - -
89N PHE* 4.0 10.3 - - + -
521N HEC 3.6 52.2 - - + -
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Residues in contact with ILE 44 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40N LEU* 3.0 46.8 + - + +
41N VAL* 3.8 4.9 - - + +
43N GLN* 1.3 77.8 - - + +
45N VAL* 1.3 68.4 + - + +
47N GLY* 3.8 0.3 - - - -
48N ILE* 3.1 47.2 + - + +
187N PRO* 4.2 30.7 - - + +
188N PHE* 4.7 19.7 - - + -
191N ALA* 5.1 5.6 - - + -
521N HEC 4.1 9.8 - - + +
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Residues in contact with VAL 45 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41N VAL* 2.8 41.6 + - + +
42N ILE* 4.1 3.4 - - - +
44N ILE* 1.3 79.3 - - + +
46N THR* 1.3 66.3 + - + +
48N ILE* 3.3 5.4 + - + +
49N PHE* 3.1 42.6 + - + -
78P PHE* 4.0 22.4 - - + -
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Residues in contact with THR 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42N ILE* 2.8 39.2 + - + +
43N GLN* 3.7 0.5 - - - -
45N VAL* 1.3 75.1 - - + +
47N GLY* 1.3 56.2 + - - +
49N PHE* 3.3 2.5 + - - +
50N MET* 2.9 33.8 + - - +
78N LEU* 4.2 18.0 - - + +
81N LEU* 4.3 17.0 - - + -
82N HIS* 2.8 31.5 + - - +
78P PHE* 4.1 28.5 - - + -
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Residues in contact with GLY 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43N GLN 2.8 18.7 + - - -
45N VAL 3.2 0.2 - - - -
46N THR* 1.3 76.3 + - - +
48N ILE* 1.3 51.3 + - - +
50N MET* 3.1 7.3 + - - +
51N ALA* 2.8 34.7 + - - +
82N HIS* 3.9 4.7 - - - -
521N HEC 3.4 34.4 - - - +
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Residues in contact with ILE 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C ALA* 4.5 2.5 - - + +
182C LEU* 4.7 7.9 - - + -
185C LEU* 3.7 36.8 - - + -
44N ILE* 3.1 34.8 + - + +
45N VAL* 3.8 5.6 - - - +
47N GLY* 1.3 73.8 - - - +
49N PHE* 1.3 67.8 + - + +
51N ALA* 3.3 16.0 + - - +
52N MET* 3.5 25.7 + - + +
184N TYR* 4.2 21.8 - - + +
188N PHE* 4.6 2.7 - - + -
521N HEC 3.5 14.5 - - + +
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Residues in contact with PHE 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45N VAL* 3.1 31.6 + - + +
46N THR 3.7 7.6 - - - +
48N ILE* 1.3 80.1 - - + +
50N MET* 1.3 62.2 + - - +
52N MET* 3.4 36.5 + - + +
53N HIS* 3.7 9.5 + - - -
78N LEU* 4.0 16.9 - - + +
78P PHE* 3.6 49.8 - + + -
79P ILE* 4.6 5.6 - - + -
81P SER* 3.7 16.4 + - - -
82P MET* 4.0 25.4 - - + -
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Residues in contact with MET 50 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46N THR 2.9 19.5 + - - +
47N GLY* 3.6 2.7 - - - +
49N PHE* 1.3 76.0 - - - +
51N ALA* 1.3 53.0 + - - +
53N HIS* 2.8 31.9 + - - +
54N TYR 3.2 8.3 + - - -
68N ILE* 3.8 21.4 - - + +
78N LEU* 3.8 22.0 - - + +
79N ARG* 3.7 22.2 - - - -
82N HIS* 3.3 37.7 - - + +
521N HEC 3.0 52.0 - - + +
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Residues in contact with ALA 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C SER* 6.2 0.2 - - - -
177C GLN* 4.2 6.8 - - - +
181C ALA* 4.1 14.4 - - + +
47N GLY 2.8 19.9 + - - +
48N ILE* 3.4 10.1 - - - +
50N MET* 1.3 72.9 - - - +
52N MET* 1.3 60.5 + - - +
53N HIS 3.0 1.9 + - - -
54N TYR* 3.3 25.7 + - - +
180N PHE* 4.0 14.5 - - + -
184N TYR* 4.5 2.9 - - + -
521N HEC 3.8 22.8 - - + +
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Residues in contact with MET 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C PRO* 4.4 5.5 - - - +
177C GLN* 3.5 22.7 - - - +
178C ARG* 3.7 36.5 + - + +
181C ALA* 4.2 6.3 - - + -
182C LEU* 3.8 26.0 - - + -
48N ILE* 3.6 26.2 - - + +
49N PHE* 3.6 32.3 - - + +
50N MET 3.0 0.8 + - - -
51N ALA* 1.3 75.3 - - - +
53N HIS* 1.3 71.5 + - + +
82P MET* 3.8 39.5 - - + -
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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
------------------------------------------------------------
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