Contacts of the helix formed by residues 31 - 52 (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 31 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ASN 4.0 3.1 - - - +
28C TYR* 2.9 42.1 + - - +
30C TRP* 1.3 78.5 - - - +
32C MET* 1.3 65.2 + - + +
33C GLY 3.2 2.9 - - - -
34C SER* 3.1 22.7 + - - +
35C LEU* 3.4 9.4 + - - +
225C PHE* 5.4 2.8 - - - -
228C LYS* 3.0 30.5 + - - +
229C ASP* 3.5 20.2 - - - +
232C THR* 2.8 32.0 + - + +
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Residues in contact with MET 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 TYR 3.7 16.6 - - - +
29C TRP* 3.2 26.9 - - + +
30C TRP 3.3 0.8 - - - -
31C ASN* 1.3 84.5 - - + +
33C GLY* 1.3 61.8 + - - +
35C LEU* 3.2 19.8 + - + +
36C LEU* 3.0 25.6 + - - +
92C VAL* 3.7 19.8 - - + +
95C MET* 4.1 30.1 - - + +
96C HIS* 3.6 37.2 - - + +
99C LYS* 5.4 0.4 - - + -
232C THR* 5.1 5.6 - - + -
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Residues in contact with GLY 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TRP 4.0 0.4 + - - -
31C ASN 3.2 1.4 - - - -
32C MET* 1.3 75.4 - - - +
34C SER* 1.3 65.3 + - - +
36C LEU* 3.1 7.3 + - - +
37C GLY* 3.1 18.0 + - - -
96C HIS* 3.6 7.6 + - - -
502C HEC 3.3 52.9 + - - +
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Residues in contact with SER 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TRP 5.1 1.4 + - - -
31C ASN* 3.1 12.9 + - - +
33C GLY* 1.3 74.0 - - - +
35C LEU* 1.3 73.5 + - - +
37C GLY* 3.1 3.6 + - - +
38C LEU* 3.0 21.8 + - - +
229C ASP* 3.3 35.5 + - - +
233C VAL* 4.7 5.0 - - - +
502C HEC 4.3 6.5 - - - +
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Residues in contact with LEU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ASN 3.4 4.7 + - - +
32C MET* 3.2 36.0 + - + +
33C GLY 3.1 0.8 - - - -
34C SER* 1.3 91.6 + - - +
36C LEU* 1.3 56.9 + - - +
38C LEU* 3.1 9.4 + - + +
39C CYS* 2.9 33.6 + - - -
92C VAL* 3.7 17.9 - - + -
232C THR* 3.9 33.0 - - - +
233C VAL* 3.9 22.2 - - + -
236C PHE* 4.1 25.9 - - + -
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Residues in contact with LEU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C MET 3.0 15.0 + - - +
33C GLY 3.1 6.0 + - - +
35C LEU* 1.3 72.1 - - - +
37C GLY* 1.3 67.9 + - - +
39C CYS* 3.3 4.4 + - - +
40C LEU* 3.1 22.3 + - - +
89C PHE* 3.5 33.1 - - + +
92C VAL* 3.9 8.1 - - + -
93C MET* 3.5 31.9 - - + +
96C HIS* 3.5 45.5 - - + +
502C HEC 3.8 33.0 - - + +
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Residues in contact with GLY 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C GLY 3.1 12.7 + - - -
34C SER* 3.1 5.8 + - - -
36C LEU* 1.3 78.4 - - - +
38C LEU* 1.3 59.9 + - - +
40C LEU* 3.2 9.9 + - - +
41C VAL* 3.2 26.7 + - - +
194C VAL* 6.2 1.1 - - - -
502C HEC 3.8 10.9 - - - +
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Residues in contact with LEU 38 (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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34C SER 3.0 11.6 + - - +
35C LEU* 3.1 12.5 + - + +
37C GLY* 1.3 71.8 - - - +
39C CYS* 1.3 65.0 + - - +
41C VAL* 3.1 12.0 + - + +
42C ILE* 2.8 48.4 + - + +
233C VAL* 3.7 25.1 - - + -
236C PHE* 4.4 17.5 - - + -
237C MET* 3.6 32.1 - - + -
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Residues in contact with CYS 39 (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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35C LEU 2.9 22.0 + - - -
36C LEU* 3.3 8.5 + - - +
38C LEU* 1.3 75.2 - - - +
40C LEU* 1.3 54.0 + - - +
42C ILE* 3.2 10.1 + - - +
43C GLN* 2.7 40.6 + - + +
85C GLY* 4.8 4.5 - - - +
88C PHE 4.6 0.7 - - - -
89C PHE* 3.6 44.4 - - + -
92C VAL* 4.7 3.6 - - - -
236C PHE* 3.6 30.5 - - - -
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Residues in contact with LEU 40 (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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36C LEU 3.1 12.0 + - - +
37C GLY* 3.4 11.9 - - - +
39C CYS* 1.3 75.7 - - - +
41C VAL* 1.3 58.7 + - + +
43C GLN* 3.6 2.2 - - - +
44C ILE* 2.8 49.2 + - + +
89C PHE* 4.1 17.6 - - + -
187C PRO 4.7 0.9 - - - +
190C ILE* 4.2 19.1 - - + -
191C ALA* 3.9 35.2 - - + +
194C VAL* 4.3 12.3 - - + -
501C HEC 4.1 25.6 - - + -
502C HEC 5.2 2.5 - - + -
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Residues in contact with VAL 41 (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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37C GLY 3.3 17.3 - - - +
38C LEU* 3.1 12.7 + - + +
40C LEU* 1.3 75.6 - - + +
42C ILE* 1.3 65.3 + - + +
44C ILE* 3.0 8.2 + - - -
45C VAL* 2.7 43.3 + - + +
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Residues in contact with ILE 42 (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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38C LEU* 2.8 44.5 + - + +
39C CYS* 3.6 8.7 - - - +
41C VAL* 1.3 72.0 - - + +
43C GLN* 1.3 67.8 + - - +
45C VAL* 3.9 3.8 - - - +
46C THR* 2.8 49.9 + - + +
81C LEU* 4.0 25.1 - - + +
85C GLY* 5.4 1.3 - - - -
236C PHE* 4.3 19.1 - - + -
237C MET* 5.9 3.6 - - + -
240C LEU* 4.5 12.8 - - + -
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Residues in contact with GLN 43 (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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39C CYS* 2.7 28.2 + - - +
40C LEU 3.6 3.1 - - - +
42C ILE* 1.3 79.7 - - - +
44C ILE* 1.3 58.7 + - - +
46C THR* 3.1 3.8 + - - -
47C GLY* 2.8 26.7 + - - -
81C LEU 3.8 6.1 + - - -
82C HIS* 3.2 36.6 + - - +
85C GLY* 3.3 26.3 - - - +
86C ALA* 3.5 12.7 + - - -
89C PHE* 4.2 12.1 - - + -
501C HEC 3.3 50.4 - - + -
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Residues in contact with ILE 44 (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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40C LEU* 2.8 49.8 + - + +
41C VAL* 3.5 5.4 - - - +
43C GLN* 1.3 75.3 - - + +
45C VAL* 1.3 62.8 + - + +
47C GLY* 3.6 0.5 - - - -
48C ILE* 3.0 53.1 + - + +
187C PRO* 4.2 19.5 - - + +
188C PHE* 4.9 17.3 - - + -
191C ALA* 5.1 5.8 - - + -
501C HEC 3.8 22.8 - - + +
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Residues in contact with VAL 45 (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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41C VAL* 2.7 43.3 + - + +
42C ILE* 3.9 3.4 - - - +
44C ILE* 1.3 73.9 - - + +
46C THR* 1.3 67.3 + - + +
47C GLY 3.0 1.3 - - - -
48C ILE* 3.2 6.4 + - - +
49C PHE* 3.1 47.6 + - + -
78E PHE* 4.3 17.9 - - + -
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Residues in contact with THR 46 (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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42C ILE* 2.8 42.5 + - + +
43C GLN* 3.7 2.1 - - - -
45C VAL* 1.3 73.7 - - + +
47C GLY* 1.3 62.0 + - - +
49C PHE* 3.4 3.8 + - - +
50C MET* 3.1 27.8 + - - +
78C LEU* 4.1 17.9 - - + +
81C LEU* 4.2 21.8 - - + -
82C HIS* 2.8 30.0 + - - +
78E PHE* 4.1 27.4 - - + -
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Residues in contact with GLY 47 (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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43C GLN 2.8 18.7 + - - -
45C VAL 3.0 0.2 - - - -
46C THR* 1.3 75.9 + - - +
48C ILE* 1.3 64.5 + - - +
50C MET* 3.0 7.1 + - - +
51C ALA 2.9 19.1 + - - -
82C HIS* 3.6 6.5 - - - -
501C HEC 3.5 36.1 - - - +
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Residues in contact with ILE 48 (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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44C ILE* 3.0 35.6 + - + +
45C VAL* 3.9 7.0 - - - +
47C GLY* 1.3 72.5 - - - +
49C PHE* 1.3 65.5 - - + +
51C ALA* 3.2 15.9 + - - +
52C MET* 3.5 15.8 + - + +
184C TYR* 3.9 21.3 - - + +
188C PHE* 4.8 2.2 - - + -
501C HEC 3.6 16.3 - - + +
181N ALA* 4.6 2.3 - - + +
182N LEU* 4.5 18.6 - - + -
185N LEU* 3.7 37.9 - - + -
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Residues in contact with PHE 49 (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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45C VAL* 3.1 42.4 + - + +
46C THR 3.8 3.6 - - - +
48C ILE* 1.3 83.4 - - + +
50C MET* 1.3 59.8 + - - +
52C MET* 3.6 25.8 - - + +
53C HIS* 3.6 18.9 + - - -
78C LEU* 4.0 18.2 - - + +
78E PHE* 3.6 45.8 - + + -
79E ILE* 4.5 4.0 - - + -
81E SER* 3.6 17.7 + - - -
82E MET* 3.9 23.6 - - + -
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Residues in contact with MET 50 (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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46C THR 3.1 18.2 + - - +
47C GLY* 3.0 7.6 + - - +
49C PHE* 1.3 72.8 - - - +
51C ALA* 1.3 57.9 + - - +
52C MET 2.9 2.2 - - - -
53C HIS* 2.7 30.5 + - - +
54C TYR* 3.0 10.7 + - - +
68C ILE* 4.0 22.5 - - + +
78C LEU* 3.7 23.8 - - + +
79C ARG* 3.8 20.2 - - - -
82C HIS* 3.3 42.8 - - + +
501C HEC 3.1 41.1 - - + +
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Residues in contact with ALA 51 (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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47C GLY 2.9 11.2 + - - +
48C ILE 3.2 11.8 + - - +
50C MET* 1.3 76.6 - - - +
52C MET* 1.3 58.8 + - - +
53C HIS 3.0 5.7 + - - -
54C TYR* 3.4 23.6 + - - +
180C PHE* 4.1 13.6 - - + -
184C TYR* 4.2 4.7 - - + -
501C HEC 3.7 24.0 - - + +
177N GLN* 4.0 8.3 - - - +
181N ALA* 4.1 15.1 - - + +
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Residues in contact with MET 52 (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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48C ILE* 3.5 20.0 - - + +
49C PHE* 3.6 37.0 - - + +
50C MET 2.9 1.0 - - - -
51C ALA* 1.3 77.0 - - - +
53C HIS* 1.3 73.7 + - + +
82E MET* 4.0 34.3 - - + -
174N PRO* 4.5 5.5 - - - +
177N GLN* 4.0 17.4 - - - +
178N ARG* 3.7 42.4 + - + +
181N ALA* 4.0 7.0 - - + -
182N LEU* 4.0 24.9 - - + -
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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