Contacts of the helix formed by residues 64 - 84 (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 PRO 64 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G ARG 3.6 3.5 - - - +
63G LEU* 1.3 86.4 - - + +
65G GLU* 1.3 69.1 + - - +
66G ASP* 3.0 4.9 + - + +
67G GLU* 3.0 33.7 + - + +
68G SER* 3.2 6.4 + - - -
106G TYR* 2.9 30.3 - - + +
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Residues in contact with GLU 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G LEU 3.4 4.4 + - - -
64G PRO* 1.3 70.6 - - - +
66G ASP* 1.3 66.5 + - - +
68G SER* 3.2 8.5 + - - -
69G TYR* 3.0 60.8 + - + +
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Residues in contact with ASP 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D PHE* 5.7 0.3 - - - -
304D PRO* 4.9 6.1 - - - +
305D PRO* 3.3 32.7 - - - +
306D LYS 4.8 5.9 - - - +
64G PRO* 3.0 3.7 + - + +
65G GLU* 1.3 80.0 - - - +
67G GLU* 1.3 66.6 + - + +
69G TYR* 3.4 7.8 + - - +
70G ALA* 3.1 23.7 + - - +
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Residues in contact with GLU 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G LYS* 5.3 7.4 + - - -
63G LEU* 3.9 20.3 - - + +
64G PRO* 3.0 24.3 + - + +
66G ASP* 1.3 77.2 - - + +
68G SER* 1.3 56.9 + - - +
70G ALA* 3.6 9.8 - - - +
71G ARG* 3.0 30.1 + - - +
74G ARG* 4.8 7.4 + - - -
102G TYR* 3.8 33.9 - - + +
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Residues in contact with SER 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G LEU 5.0 5.0 + - - -
63G LEU* 3.7 22.7 - - - +
64G PRO 3.2 9.2 + - - -
65G GLU* 3.2 13.4 + - - -
66G ASP 3.1 0.4 - - - -
67G GLU* 1.3 75.3 - - - +
69G TYR* 1.3 68.5 + - - +
71G ARG* 3.1 8.3 + - - +
72G ALA* 2.9 22.5 + - - +
19H PRO* 4.1 20.1 - - - +
20H LYS 5.2 3.2 + - - -
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Residues in contact with TYR 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A THR* 3.5 21.2 - - + +
302D PHE* 4.0 11.6 - - + -
305D PRO* 3.5 28.3 - - + -
65G GLU* 3.0 57.6 + - + +
66G ASP* 3.4 9.2 + - - +
68G SER* 1.3 75.7 - - - +
70G ALA* 1.3 62.5 + - - +
72G ALA* 3.1 9.2 - - - +
73G TYR* 3.1 21.3 + - - +
20H LYS* 3.3 36.3 - - + +
22H LYS* 3.4 44.7 - - + +
24H ILE* 4.0 3.3 - - - +
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Residues in contact with ALA 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D PHE* 3.9 20.4 - - + -
66G ASP 3.1 17.6 + - - +
67G GLU* 3.6 12.1 - - - +
68G SER 3.1 0.2 - - - -
69G TYR* 1.3 76.7 - - - +
71G ARG* 1.3 63.7 + - - +
73G TYR* 3.1 6.4 + - - +
74G ARG* 3.0 38.9 + - - +
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Residues in contact with ARG 71 (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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213C THR* 4.1 5.1 - - - +
216C LEU* 5.2 0.2 - - - +
46G ASP 4.7 6.3 + - - -
47G ASP* 3.8 17.8 + - - +
49G ILE 5.3 1.6 + - - -
51G GLU* 3.1 27.1 + - - +
56G MET* 4.8 5.9 - - - +
60G LEU* 3.2 38.2 - - - +
63G LEU* 4.7 4.5 - - - -
67G GLU 3.0 19.0 + - - +
68G SER* 3.4 7.5 + - - +
70G ALA* 1.3 74.9 - - - +
72G ALA* 1.3 63.7 - - - +
74G ARG* 3.3 15.3 + - - +
75G ILE* 3.1 57.3 + - + +
102G TYR* 3.1 31.2 + - + +
103G LEU* 4.9 0.6 - - - +
19H PRO* 4.3 20.6 - - - +
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Residues in contact with ALA 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C LEU* 3.5 26.1 - - + +
68G SER 2.9 12.7 + - - +
69G TYR* 3.1 15.7 - - - +
70G ALA 3.1 0.2 - - - -
71G ARG* 1.3 78.6 - - - +
73G TYR* 1.3 66.2 + - - +
75G ILE* 3.2 1.2 + - - -
76G ILE* 3.1 25.4 + - + +
19H PRO* 5.1 9.9 - - + -
20H LYS 5.1 2.7 - - - +
21H GLN* 4.7 12.3 - - + -
24H ILE* 4.5 9.4 - - + -
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Residues in contact with TYR 73 (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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300D PHE* 3.7 35.4 + + + +
301D VAL* 4.4 1.1 - - - -
302D PHE* 3.6 50.5 + + + -
69G TYR 3.1 6.6 + - - +
70G ALA 3.1 8.7 + - - +
72G ALA* 1.3 78.5 - - - +
74G ARG* 1.3 69.5 + - + +
76G ILE* 3.0 8.0 + - + +
77G ARG* 2.8 69.8 + - + +
92G GLU* 5.5 1.9 + - - -
24H ILE* 3.8 29.5 - - + +
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Residues in contact with ARG 74 (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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41G LEU 4.6 0.2 - - - +
42G GLY 3.5 25.6 - - - +
43G LEU* 3.4 10.9 - - + +
44G LYS* 3.9 31.2 - - - +
47G ASP* 2.7 43.9 + - - +
67G GLU* 4.8 6.5 + - - -
70G ALA* 3.0 33.5 + - - +
71G ARG* 3.5 18.3 - - - +
73G TYR* 1.3 83.9 - - + +
75G ILE* 1.3 57.5 + - - +
77G ARG* 3.5 17.7 - - - +
78G ALA 3.0 22.2 + - - -
94G ILE* 4.6 5.4 - - - -
102G TYR* 3.2 25.7 + - - -
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Residues in contact with ILE 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C ILE* 3.4 30.5 - - + -
213C THR* 4.0 15.7 - - + +
216C LEU* 4.1 16.6 - - + -
43G LEU* 4.1 5.6 - - + -
47G ASP* 4.5 16.4 - - + +
71G ARG* 3.1 57.0 + - + +
72G ALA 3.6 6.5 - - - +
73G TYR 3.2 0.2 - - - -
74G ARG* 1.3 73.4 - - - +
76G ILE* 1.3 67.3 + - - +
78G ALA* 3.2 5.6 + - - +
79G HIS* 3.1 33.8 + - + +
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Residues in contact with ILE 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C LEU* 3.8 22.9 - - + +
217C ASP* 4.4 14.3 - - + +
300D PHE* 3.4 39.3 - - + -
72G ALA 3.1 20.3 + - - +
73G TYR* 3.0 6.4 + - + +
75G ILE* 1.3 74.3 - - - +
77G ARG* 1.3 65.6 + - - +
79G HIS* 2.9 20.6 + - - +
80G GLN* 2.9 12.1 + - - +
21H GLN* 3.9 32.3 - - + +
24H ILE* 4.4 20.0 - - + -
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Residues in contact with ARG 77 (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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300D PHE* 5.6 5.8 - - + -
41G LEU 4.0 7.6 - - - -
42G GLY* 3.3 25.9 + - - -
73G TYR* 2.8 58.2 + - + +
74G ARG* 3.5 19.3 - - - +
76G ILE* 1.3 76.5 - - - +
78G ALA* 1.3 53.2 + - - +
80G GLN* 3.3 7.4 + - - +
81G THR* 2.8 37.2 + - - +
88G LEU* 3.6 38.6 - - + +
92G GLU* 4.2 28.4 + - - +
94G ILE* 4.9 4.9 - - - +
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Residues in contact with ALA 78 (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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210C LEU* 3.7 19.2 - - + +
212C ILE* 5.2 0.4 - - + -
41G LEU* 4.0 16.9 + - + +
43G LEU* 3.7 26.2 - - + -
74G ARG 3.0 14.9 + - - +
75G ILE* 3.2 10.8 - - - +
76G ILE 3.1 0.2 - - - -
77G ARG* 1.3 77.2 - - - +
79G HIS* 1.3 57.1 + - - +
81G THR* 3.8 3.5 - - - -
82G GLU* 2.9 31.2 + - - +
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Residues in contact with HIS 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PRO* 5.6 1.5 - - + +
24C SER* 3.8 18.2 - - - +
25C SER* 2.7 32.4 + - - +
208C ASN* 3.7 17.6 + - - -
210C LEU* 3.4 21.4 - - + +
212C ILE* 4.1 5.3 - - + +
213C THR 3.2 26.7 - - - -
214C GLY* 4.1 13.2 + - - -
216C LEU* 5.8 1.6 - - + +
217C ASP* 4.7 9.2 + - + +
75G ILE* 3.1 26.1 + - + +
76G ILE* 2.9 10.9 + - - +
78G ALA* 1.3 80.0 - - - +
80G GLN* 1.3 57.2 + - - +
82G GLU* 3.4 0.4 + - - -
83G LEU* 2.9 34.6 + - - +
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Residues in contact with GLN 80 (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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24C SER* 5.1 0.2 + - - -
295D ILE 3.1 20.8 + - - +
296D LYS 3.2 13.3 + - - -
298D ARG* 2.9 60.7 + - - +
299D LYS* 5.7 0.2 - - - -
300D PHE* 3.9 23.8 - - + -
76G ILE 2.9 12.0 + - - +
77G ARG* 3.7 8.1 - - - +
79G HIS* 1.3 74.7 - - - +
81G THR* 1.3 60.9 + - - +
83G LEU* 3.4 10.3 - - - +
84G THR* 2.9 41.0 + - + +
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Residues in contact with THR 81 (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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41G LEU* 4.8 11.0 - - + -
77G ARG* 2.8 22.4 + - - +
78G ALA* 3.8 5.3 - - - -
80G GLN* 1.3 77.6 - - - +
82G GLU* 1.3 63.1 + - - +
84G THR* 2.5 26.0 + - - +
85G HIS 3.0 5.9 + - - -
86G HIS* 3.2 31.7 + - + +
87G LEU* 3.8 16.8 - - - +
88G LEU* 3.4 27.7 - - + +
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Residues in contact with GLU 82 (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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25C SER* 4.1 15.7 - - - +
27C ASN* 5.1 4.2 + - - +
209C PRO* 4.1 20.6 - - + +
210C LEU* 3.6 30.3 - - + +
317C THR* 5.3 6.3 - - - +
41G LEU* 4.3 12.8 - - + +
78G ALA 2.9 18.8 + - - +
79G HIS* 3.8 4.5 - - - +
81G THR* 1.3 76.0 - - - +
83G LEU* 1.3 58.6 + - - +
85G HIS* 2.9 43.3 + - - +
86G HIS 4.9 2.2 - - - -
51H ARG* 4.8 13.1 + - - -
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Residues in contact with LEU 83 (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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24C SER* 3.5 50.5 - - - +
25C SER* 4.0 8.7 - - - +
292D TRP* 4.9 5.6 - - + -
295D ILE* 3.7 26.7 - - + +
296D LYS* 3.4 33.1 + - + -
298D ARG* 3.9 1.1 - - - +
79G HIS 2.9 14.2 + - - +
80G GLN* 3.4 30.1 - - - +
81G THR 3.2 0.4 - - - -
82G GLU* 1.3 75.3 - - - +
84G THR* 1.3 72.8 + - + +
85G HIS* 3.3 7.3 + - - -
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Residues in contact with THR 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D LYS* 3.3 37.4 + - + +
80G GLN* 2.9 31.2 + - + +
81G THR* 2.5 24.7 + - - +
83G LEU* 1.3 83.8 - - + +
85G HIS* 1.3 68.4 + - - +
86G HIS* 3.2 31.4 + - - +
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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
------------------------------------------------------------
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