Contacts of the helix formed by residues 62 - 75 (chain D) in PDB entry 1KR2
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 62 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D ASP* 3.3 13.7 - - - +
61D ILE* 1.4 92.6 - - + +
63D ALA* 1.3 65.2 + - - +
64D TYR* 3.2 35.4 - - + +
65D HIS* 3.1 25.8 + - + +
66D ARG* 3.3 8.5 + - - +
261D ARG* 3.8 27.5 - - - +
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Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D PRO* 6.0 0.2 - - + -
51D VAL 4.3 7.0 - - - +
52D GLY* 4.6 0.4 - - - -
53D ASP* 2.8 25.5 + - - +
61D ILE 3.5 0.2 + - - -
62D PRO* 1.3 71.6 - - - +
64D TYR* 1.3 58.4 + - - +
66D ARG* 3.0 26.4 + - - +
67D VAL* 2.7 37.4 + - + +
87D SER* 4.4 20.4 - - - +
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Residues in contact with TYR 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D ASP* 5.9 0.2 - - - -
62D PRO* 3.2 27.0 - - + +
63D ALA* 1.3 78.1 - - - +
65D HIS* 1.3 103.8 + + - +
67D VAL* 4.0 5.5 - - - +
68D ILE* 3.0 48.2 + - + +
247D TYR* 4.7 0.4 - - - -
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Residues in contact with HIS 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ILE* 3.8 15.4 - - + +
62D PRO* 3.1 24.0 + - + +
64D TYR* 1.3 117.9 - + - +
66D ARG* 1.3 57.7 + - - +
68D ILE* 3.3 1.7 + - - +
69D MET* 3.0 35.5 + - - +
247D TYR* 2.8 39.9 + + - -
251D HIS* 4.5 12.1 + + - +
253D LEU* 3.5 29.1 - - + +
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Residues in contact with ARG 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D SER 2.9 30.4 + - - +
17D PHE* 3.5 18.6 - - - +
18D ASN* 3.6 21.5 - - - +
20D ILE* 5.7 0.7 - - - +
50D PRO* 4.1 10.3 - - + +
51D VAL* 2.9 37.6 + - - +
52D GLY 3.9 1.8 - - - -
53D ASP* 3.3 23.4 + - - -
60D LEU* 3.4 20.7 - - - +
61D ILE* 2.9 33.4 + - + -
62D PRO 3.3 1.4 + - - +
63D ALA* 3.0 13.9 + - - +
65D HIS* 1.3 77.5 - - - +
67D VAL* 1.3 55.5 + - - +
69D MET* 3.6 12.1 - - + +
70D ALA* 3.0 29.1 + - - +
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D PRO* 4.1 22.9 - - + -
63D ALA* 2.7 26.3 + - + +
64D TYR* 4.0 5.8 - - - +
66D ARG* 1.3 68.8 - - - +
68D ILE* 1.3 69.1 + - + +
70D ALA* 3.2 7.7 + - - +
71D GLU* 2.9 46.0 + - + +
82D VAL* 4.4 3.6 - - + -
84D THR* 3.9 19.1 - - + -
87D SER* 4.0 22.4 - - - +
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Residues in contact with ILE 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D TYR* 3.0 36.3 + - + +
65D HIS 3.8 3.1 - - - +
67D VAL* 1.3 80.8 - - + +
69D MET* 1.3 56.6 + - - +
71D GLU* 3.1 17.0 + - - +
72D LEU* 2.8 37.7 + - + +
247D TYR* 3.4 43.1 - - + +
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Residues in contact with MET 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PHE 4.6 0.7 - - - +
19D PRO* 4.0 13.5 - - + -
20D ILE* 4.1 7.6 - - + -
61D ILE* 4.3 1.3 - - + -
65D HIS 3.0 25.7 + - - +
66D ARG* 3.6 20.2 - - + +
68D ILE* 1.3 75.5 - - - +
70D ALA* 1.3 58.2 + - - +
72D LEU* 3.3 7.5 + - - +
73D ALA* 2.9 29.5 + - - +
244D VAL* 3.5 20.2 - - + +
247D TYR* 3.4 20.9 - - + -
248D ILE* 3.7 35.2 - - - -
253D LEU* 3.7 13.5 - - + -
254D TYR* 3.8 20.4 - - - +
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PHE* 5.3 2.7 - - + -
20D ILE* 4.2 14.0 - - + +
48D ILE* 4.4 15.5 - - + -
50D PRO* 4.4 6.5 - - + -
66D ARG 3.0 19.2 + - - +
67D VAL* 3.2 8.0 + - - +
69D MET* 1.3 77.8 - - - +
71D GLU* 1.3 55.7 + - - +
73D ALA* 3.3 8.9 + - - +
74D THR* 2.9 30.7 + - - +
82D VAL* 3.5 18.6 - - + +
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Residues in contact with GLU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D VAL* 2.9 34.5 + - - +
68D ILE* 3.5 19.4 - - - +
70D ALA* 1.3 73.0 - - - +
72D LEU* 1.3 62.2 + - + +
74D THR* 3.2 8.0 + - - -
75D LYS* 2.8 30.8 + - - +
82D VAL* 3.9 19.9 - - + +
84D THR* 4.4 9.9 - - - +
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ILE* 2.8 24.6 + - + +
69D MET* 3.5 10.5 - - - +
71D GLU* 1.3 78.0 - - + +
73D ALA* 1.3 62.6 + - - +
74D THR 3.4 0.3 + - - -
75D LYS* 3.5 28.5 - - + +
76D ASN* 4.8 1.4 + - - +
241D PRO* 5.3 1.4 - - - +
243D LEU* 3.8 45.5 - - + +
244D VAL* 4.6 4.0 - - + -
247D TYR* 3.8 41.5 - - + -
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Residues in contact with ALA 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C TYR* 4.6 7.6 + - - -
20D ILE* 3.8 31.2 - - + -
25D LEU* 3.8 18.0 - - + +
69D MET 2.9 18.2 + - - +
70D ALA 3.4 6.5 - - - +
71D GLU 3.1 0.2 - - - -
72D LEU* 1.3 77.0 - - - +
74D THR* 1.3 60.4 + - - +
75D LYS 3.6 0.2 - - - -
76D ASN* 4.7 4.3 + - - +
77D SER 5.1 0.5 + - - -
241D PRO* 3.9 21.7 - - + +
244D VAL* 3.9 6.5 - - + +
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Residues in contact with THR 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LEU* 4.2 8.1 - - + -
48D ILE* 3.8 27.6 - - + -
70D ALA 2.9 17.4 + - - +
71D GLU* 3.3 10.4 + - - -
73D ALA* 1.3 79.9 - - + +
75D LYS* 1.3 55.2 + - - +
76D ASN 3.1 3.4 - - - -
77D SER* 2.8 33.7 + - - +
80D VAL* 3.3 33.3 + - + +
81D GLU* 4.4 1.1 - - - -
82D VAL* 3.7 12.6 + - + +
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Residues in contact with LYS 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D GLU 2.8 16.1 + - - +
72D LEU* 3.5 27.1 + - + +
74D THR* 1.3 71.9 - - - +
76D ASN* 1.3 72.1 + - - +
77D SER 3.4 4.2 + - - +
243D LEU* 3.9 22.4 - - + -
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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