Contacts of the helix formed by residues 60 - 74 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ARG* 2.2 40.7 + - - +
59B GLY* 1.3 74.0 + - - +
61B SER* 1.3 58.6 + - - +
62B GLU* 3.5 2.5 - - - -
63B THR* 3.3 21.3 + - + +
64B ASP* 2.9 29.3 + - - +
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Residues in contact with SER 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A VAL* 3.7 23.1 - - - -
319A VAL* 4.8 2.0 - - - -
346A TYR* 3.1 24.9 - - - -
57B VAL* 3.7 19.6 - - - +
58B ARG 3.3 15.2 + - - -
59B GLY 3.4 3.4 + - - -
60B ASP* 1.3 75.9 + - - +
62B GLU* 1.3 66.0 + - - +
64B ASP* 3.4 2.1 + - - +
65B LEU 2.9 22.7 + - - -
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A TYR* 4.7 1.1 - - - -
349A ASN* 5.5 9.7 + - - +
353A LYS* 4.1 5.8 + - - +
59B GLY 5.8 2.2 - - - +
60B ASP* 5.6 0.7 - - - -
61B SER* 1.3 83.7 + - - +
63B THR* 1.3 66.4 + - - +
65B LEU* 3.4 12.1 + - + +
66B GLU* 3.2 29.7 + - - +
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Residues in contact with THR 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ASP* 3.3 25.3 + - + +
61B SER 3.2 0.6 - - - -
62B GLU* 1.3 81.1 - - - +
64B ASP* 1.3 51.4 + - - +
66B GLU* 2.9 18.0 + - + +
67B ALA* 2.9 31.0 + - + +
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Residues in contact with ASP 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A SER* 2.6 25.7 + - - -
314A PHE* 4.8 7.1 - - - -
318A VAL* 3.3 8.4 - - + +
346A TYR* 2.5 34.8 + - - -
58B ARG* 3.2 22.6 + - - +
60B ASP* 2.9 22.7 + - - +
61B SER 3.5 3.4 - - - +
63B THR* 1.3 68.6 - - - +
65B LEU* 1.3 59.8 + - - +
67B ALA* 3.3 11.7 - - - +
68B LEU* 2.7 28.8 + - - +
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A TYR* 3.4 35.2 - - + +
349A ASN* 3.6 25.6 - - + +
350A PHE* 3.7 34.3 - - + +
353A LYS* 3.1 38.8 - - + +
61B SER 2.9 14.8 + - - +
62B GLU* 3.4 13.9 - - + +
64B ASP* 1.3 74.7 + - - +
66B GLU* 1.3 64.0 + - - +
68B LEU* 3.2 11.0 + - + +
69B PHE* 3.2 23.0 - - + -
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Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A LYS* 3.9 16.4 + - - +
62B GLU* 3.2 18.7 + - - +
63B THR* 2.9 13.2 + - + +
65B LEU* 1.3 76.8 - - - +
67B ALA* 1.3 58.3 + - - +
69B PHE* 2.9 8.7 + - - +
70B ASN* 2.8 34.9 + - - +
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A PHE* 4.5 5.6 - - + -
63B THR* 2.9 9.3 + - + +
64B ASP* 3.0 23.1 + - - +
66B GLU* 1.3 75.7 - - - +
68B LEU* 1.3 60.7 + - - +
70B ASN* 3.1 9.8 - - - +
71B ALA* 3.1 26.5 + - - +
78B ALA 6.0 0.4 - - - +
80B VAL* 3.9 17.4 - - + +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A SER* 3.8 15.9 - - - -
314A PHE* 3.9 15.7 - - + -
346A TYR* 3.8 19.3 - - - +
350A PHE* 3.8 32.8 - - + -
366A VAL* 3.8 26.6 - - + +
369A ASN* 3.6 34.2 + - + +
370A PHE* 4.1 14.4 - - + -
64B ASP 2.7 13.6 + - - +
65B LEU* 3.3 11.2 - - + +
66B GLU 3.2 0.2 - - - -
67B ALA* 1.3 74.2 - - - +
69B PHE* 1.3 62.9 + - + +
71B ALA* 3.9 8.8 - - - +
72B VAL* 4.5 1.4 + - - +
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Residues in contact with PHE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A PHE* 3.8 23.3 - + - -
353A LYS* 3.3 60.1 - - + -
354A LEU* 3.6 18.8 - - + -
357A LEU* 3.8 27.8 - - + -
366A VAL* 3.8 14.3 - - + +
65B LEU* 3.2 23.3 + - + -
66B GLU* 2.9 9.6 + - - +
68B LEU* 1.3 78.0 - - + +
70B ASN* 1.3 58.1 + - - +
71B ALA 3.0 4.9 - - - -
72B VAL* 2.7 22.3 + - - +
73B MET* 3.0 22.8 + - + +
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Residues in contact with ASN 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B GLU* 2.8 34.7 + - + +
67B ALA* 3.1 16.1 - - - +
69B PHE* 1.3 70.8 - - - +
71B ALA* 1.3 62.9 + - - +
72B VAL 3.1 0.2 - - - -
73B MET* 3.7 8.1 - - + +
74B ASN* 2.7 56.1 + - - +
77B THR 3.8 20.6 + - - -
78B ALA* 3.8 9.4 + - - +
80B VAL* 5.3 0.7 - - - +
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A PHE* 4.4 8.1 - - + -
369A ASN* 4.7 8.7 - - - +
67B ALA 3.1 19.7 + - - +
68B LEU 3.9 8.5 - - - +
69B PHE 3.0 0.6 + - - -
70B ASN* 1.3 78.2 + - - +
72B VAL* 1.3 59.8 + - + +
75B PRO* 3.3 24.9 - - - +
78B ALA* 3.9 11.6 - - - +
80B VAL* 3.7 25.1 - - + +
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Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A MET* 4.6 7.6 - - + +
365A SER* 3.6 48.2 - - - +
366A VAL* 3.9 17.5 - - + +
369A ASN* 5.5 3.4 - - - +
68B LEU 4.6 2.9 - - - +
69B PHE 2.7 15.8 + - - +
71B ALA* 1.3 77.3 - - + +
73B MET* 1.3 74.7 + - - +
74B ASN 3.3 1.2 + - - -
75B PRO* 3.9 11.6 - - - +
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Residues in contact with MET 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A LEU* 4.4 15.5 - - + -
358A PRO* 5.9 0.4 - - + -
362A MET* 3.6 34.8 - - + -
366A VAL* 5.7 1.8 - - + -
69B PHE* 3.0 25.6 + - + +
70B ASN* 3.6 3.8 + - + -
72B VAL* 1.3 89.7 - - - +
74B ASN* 1.3 67.0 + - - +
75B PRO* 4.3 0.6 - - - +
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Residues in contact with ASN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ASN* 2.7 51.1 - - - +
73B MET* 1.3 79.7 - - - +
75B PRO* 1.3 71.8 - - - +
76B LYS* 3.0 4.1 + - + -
77B THR* 2.7 34.8 + - + +
78B ALA 3.7 2.8 + - - -
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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