Contacts of the helix formed by residues 60 - 74 (chain D) in PDB entry 3KYS
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 ASP 60 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58D ARG* 2.7 41.3 + - - +
59D GLY* 1.3 72.9 + - - +
61D SER* 1.3 59.5 + - - +
62D GLU 3.3 2.2 - - - -
63D THR* 2.7 41.8 + - + +
64D ASP* 2.8 19.0 + - - +
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Residues in contact with SER 61 (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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318C VAL* 4.3 15.4 - - - +
346C TYR* 3.6 21.9 - - - -
57D VAL* 2.9 25.3 - - - +
58D ARG 2.6 22.8 + - - -
59D GLY 3.3 3.6 + - - -
60D ASP* 1.3 75.2 - - - +
62D GLU* 1.3 63.1 + - - +
64D ASP* 3.2 2.9 + - - +
65D LEU* 2.8 27.4 + - - +
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Residues in contact with GLU 62 (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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349C ASN* 6.1 2.7 - - - +
353C LYS* 4.9 2.2 + - - +
59D GLY 5.2 1.3 + - - +
60D ASP 3.3 0.4 - - - -
61D SER* 1.3 79.6 - - - +
63D THR* 1.3 64.5 + - + +
65D LEU* 3.4 7.4 + - - +
66D GLU* 3.1 31.9 + - - +
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Residues in contact with THR 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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60D ASP* 2.7 35.8 + - + +
62D GLU* 1.3 75.8 - - + +
64D ASP* 1.3 63.5 + - - +
66D GLU* 3.0 16.1 + - - +
67D ALA* 2.6 36.5 + - - +
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Residues in contact with ASP 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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313C SER* 2.5 27.3 + - - -
314C PHE* 5.0 5.2 - - - -
318C VAL* 3.1 12.2 - - + +
346C TYR* 2.9 20.6 + - + +
58D ARG* 3.1 28.0 + - - +
60D ASP* 2.8 19.3 + - - +
61D SER* 3.5 6.3 - - - +
63D THR* 1.3 79.9 + - - +
65D LEU* 1.3 60.9 + - - +
67D ALA* 3.2 9.7 + - - +
68D LEU* 2.9 22.9 + - - +
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Residues in contact with LEU 65 (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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346C TYR* 3.8 32.2 + - + +
349C ASN* 3.6 33.2 - - + +
350C PHE* 3.5 43.3 - - + +
353C LYS* 4.0 23.3 - - + +
61D SER 2.8 20.2 + - - +
62D GLU* 3.7 7.9 - - - +
64D ASP* 1.3 71.8 - - - +
66D GLU* 1.3 63.6 + - - +
68D LEU* 3.3 18.5 + - + +
69D PHE* 3.4 16.6 - - + -
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Residues in contact with GLU 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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353C LYS* 3.8 21.9 + - + +
62D GLU* 3.1 23.5 + - - +
63D THR* 3.0 15.6 + - - +
65D LEU* 1.3 76.8 - - - +
67D ALA* 1.3 62.0 + - - +
69D PHE* 3.0 8.1 + - - +
70D ASN* 2.8 36.5 + - - +
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Residues in contact with ALA 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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314C PHE* 4.4 7.0 - - + -
63D THR 2.6 20.0 + - - +
64D ASP* 3.5 11.4 - - - +
66D GLU* 1.3 70.9 - - - +
68D LEU* 1.3 63.9 + - - +
70D ASN* 3.2 9.4 - - - +
71D ALA* 2.9 27.5 + - - +
80D VAL* 4.0 17.7 - - + +
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Residues in contact with LEU 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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313C SER* 3.8 13.9 - - - -
314C PHE* 3.9 16.0 - - + -
346C TYR* 3.7 19.5 - - + +
350C PHE* 3.5 39.5 - - + -
366C VAL* 4.0 24.8 - - + +
369C ASN* 3.7 36.0 - - + +
370C PHE* 4.3 10.8 - - + -
64D ASP 2.9 10.8 + - - +
65D LEU* 3.3 11.7 - - + +
67D ALA* 1.3 76.8 - - - +
69D PHE* 1.3 61.8 + - + +
71D ALA* 3.7 10.7 - - - +
72D VAL* 4.3 1.6 + - - +
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Residues in contact with PHE 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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350C PHE* 3.5 36.6 - + - -
353C LYS* 3.3 50.3 - - + -
354C LEU* 3.4 13.9 - - + -
357C LEU* 3.6 31.0 - - + -
366C VAL* 4.2 12.2 - - + +
65D LEU* 3.4 21.1 - - + +
66D GLU* 3.0 9.7 + - - +
68D LEU* 1.3 79.9 - - + +
70D ASN* 1.3 58.8 + - - +
71D ALA 3.0 4.7 - - - -
72D VAL* 3.0 9.5 + - - +
73D MET* 2.9 32.2 + - + +
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Residues in contact with ASN 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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66D GLU* 2.8 34.3 + - - +
67D ALA* 3.2 14.6 - - - +
69D PHE* 1.3 70.0 - - - +
71D ALA* 1.3 59.2 + - - +
72D VAL 3.1 0.7 - - - -
73D MET* 3.7 10.8 - - + +
74D ASN* 2.8 59.2 + - - +
78D ALA* 3.5 11.8 - - - +
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Residues in contact with ALA 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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314C PHE* 3.9 12.3 - - + -
369C ASN* 5.0 3.4 - - - +
67D ALA 2.9 20.0 + - - +
68D LEU 3.7 9.2 - - - +
69D PHE 3.0 0.4 - - - -
70D ASN* 1.3 78.5 + - - +
72D VAL* 1.3 61.6 + - + +
75D PRO* 3.4 25.1 - - - +
78D ALA* 3.8 11.4 - - - -
80D VAL* 3.7 25.2 - - + +
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Residues in contact with VAL 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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362C MET* 4.7 4.5 - - + +
365C SER* 3.6 48.0 - - - +
366C VAL* 3.8 15.9 - - + -
369C ASN* 5.4 4.7 - - - +
68D LEU 4.6 2.7 - - - +
69D PHE 3.0 7.5 + - - +
71D ALA* 1.3 82.4 - - + +
73D MET* 1.3 82.2 + - + +
74D ASN 3.3 2.5 + - - -
75D PRO* 3.8 13.2 - - - +
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Residues in contact with MET 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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357C LEU* 3.9 30.1 - - + -
358C PRO* 6.1 0.7 - - - -
362C MET* 4.0 25.4 - - + +
366C VAL* 5.0 2.5 - - + -
69D PHE* 2.9 26.1 + - + +
70D ASN* 3.8 9.6 - - + -
72D VAL* 1.3 107.5 - - + +
74D ASN* 1.3 67.8 + - - +
75D PRO* 4.2 0.6 - - - +
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Residues in contact with ASN 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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70D ASN* 2.8 41.3 + - - +
73D MET* 1.3 84.1 + - - +
75D PRO* 1.3 72.7 - - - +
76D LYS* 3.1 3.9 + - - -
77D THR* 3.3 25.3 + - - +
78D ALA 3.2 10.6 + - - -
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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