Contacts of the helix formed by residues 63 - 77 (chain A) in PDB entry 1KEK
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 SER 63 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TYR* 3.6 21.1 - - - +
61A MET* 3.4 4.6 - - - +
62A GLN* 1.3 89.4 + - - +
64A GLU* 1.3 60.1 - - - +
65A ALA* 3.1 17.6 + - - +
66A GLY 3.1 9.5 + - - -
67A ALA* 3.0 24.9 + - - +
92A LEU* 4.4 6.3 - - - -
969A ILE* 3.7 24.2 - - - -
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 3.3 24.2 - - + +
30A ILE* 3.6 12.5 - - - +
63A SER* 1.3 73.3 - - - +
65A ALA* 1.3 59.2 + - - +
67A ALA* 3.5 7.7 - - - +
68A ALA* 2.8 30.8 + - - +
84A PHE 5.9 0.2 - - - +
85A THR* 3.5 12.3 - - - +
89A GLY* 3.3 40.2 - - - +
92A LEU* 3.9 4.4 - - + +
93A MET* 3.7 14.9 - - + +
969A ILE* 4.1 1.2 - - - +
2236A HTL 2.7 47.8 + - - +
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN* 5.6 0.7 - - - +
63A SER* 3.1 9.4 + - - +
64A GLU* 1.3 79.8 - - - +
66A GLY* 1.3 55.1 + - - +
68A ALA* 3.4 4.2 + - - +
69A GLY* 3.0 24.3 + - - -
92A LEU* 3.6 33.5 - - + +
96A ASN* 4.2 5.2 + - - +
92B LEU* 6.3 2.9 - - + -
870B GLU* 5.7 9.4 - - + -
871B ASP* 4.9 2.9 - - + +
874B GLU* 4.4 4.3 - - - +
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Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A MET* 3.6 8.2 - - - +
62A GLN* 3.5 17.8 - - - +
63A SER* 3.1 10.1 + - - -
65A ALA* 1.3 71.6 - - - +
67A ALA* 1.3 64.4 + - - +
69A GLY 3.3 0.7 + - - -
70A ALA* 2.9 23.2 + - - +
874B GLU* 3.4 31.5 + - - +
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 3.5 25.6 - - - +
27A ILE 4.4 9.0 - - - +
28A TYR* 4.7 0.7 - - + -
61A MET* 3.5 15.8 - - + +
63A SER 3.0 14.6 + - - +
64A GLU* 3.5 12.8 - - - +
66A GLY* 1.3 77.0 - - - +
68A ALA* 1.3 57.8 + - - +
70A ALA 3.3 1.2 + - - -
71A VAL* 2.9 33.9 + - - +
83A THR* 4.5 0.4 - - - +
93A MET* 4.2 10.5 - - + -
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLU 2.8 20.2 + - - +
65A ALA* 3.8 4.0 - - - +
66A GLY 3.3 0.2 - - - -
67A ALA* 1.3 72.9 - - - +
69A GLY* 1.3 58.1 + - - +
71A VAL* 3.6 8.0 - - - +
72A HIS* 2.9 29.6 + - - +
92A LEU 5.0 0.2 - - - +
93A MET* 3.8 32.5 - - + +
96A ASN* 3.6 24.8 - - + +
100A ILE* 4.2 1.4 - - - +
109A PHE* 4.9 6.1 - - + -
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Residues in contact with GLY 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ALA 3.0 14.2 + - - -
66A GLY 3.8 2.5 - - - -
68A ALA* 1.3 76.2 - - - +
70A ALA* 1.3 55.5 + - - +
72A HIS* 3.2 4.5 + - - +
73A GLY 2.9 23.4 + - - -
96A ASN* 3.4 18.1 - - - +
871B ASP* 3.8 11.0 - - - -
874B GLU* 3.7 15.9 - - - -
875B TYR* 3.6 7.1 - - - -
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 6.3 0.2 - - - -
26A ALA* 3.7 17.3 - - + -
61A MET* 4.3 15.7 - - + -
66A GLY 2.9 16.2 + - - +
67A ALA 3.6 4.5 - - - +
69A GLY* 1.3 75.2 - - - +
71A VAL* 1.3 56.8 + - - +
73A GLY 3.1 0.9 + - - -
74A ALA* 2.9 29.8 + - - +
874B GLU* 3.2 18.4 + - - +
877B PHE* 4.6 0.2 - - + -
878B GLY* 3.2 14.5 - - - +
881B MET* 4.3 8.1 - - - -
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 3.9 14.6 - - + -
67A ALA 2.9 22.6 + - - +
68A ALA* 3.6 6.7 - - - +
70A ALA* 1.3 75.9 - - - +
72A HIS* 1.3 66.1 + - - +
74A ALA* 4.0 0.7 - - - +
75A LEU* 3.0 44.2 + - + +
81A THR* 3.8 27.4 - - + +
82A THR 4.0 2.7 - - - +
83A THR* 3.9 25.8 - - + -
100A ILE* 4.2 3.1 - - + -
107A GLY* 5.5 0.4 - - - -
109A PHE* 4.0 22.4 - - + -
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Residues in contact with HIS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ALA 2.9 10.3 + - - +
69A GLY 3.2 8.0 + - - +
71A VAL* 1.3 78.6 - - - +
73A GLY* 1.3 57.7 + - - +
75A LEU* 3.4 2.4 + - - +
76A ALA* 2.9 25.7 + - + +
96A ASN* 3.0 18.5 + - - +
99A LYS* 3.7 21.5 + - + +
100A ILE* 3.9 18.6 - - + -
103A GLU* 2.8 27.5 + - - -
105A LEU* 3.7 17.0 - - + -
867B SER* 2.7 42.1 + - - -
875B TYR* 3.5 14.9 + + - -
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Residues in contact with GLY 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLY 2.9 12.5 + - - -
70A ALA 3.1 1.3 + - - -
72A HIS* 1.3 77.1 - - - +
74A ALA* 1.3 56.8 + - - +
76A ALA* 3.3 2.8 + - - +
77A ALA* 3.0 31.2 + - - +
875B TYR* 3.4 37.4 - - - -
879B MET* 3.6 12.0 - - - +
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 4.1 22.2 - - + -
70A ALA 2.9 14.8 + - - +
71A VAL 4.0 1.6 - - - +
73A GLY* 1.3 75.2 - - - +
75A LEU* 1.3 60.7 + - - +
77A ALA 3.3 2.9 + - - -
78A GLY 3.2 5.7 + - - -
79A ALA* 2.9 22.7 + - + -
81A THR* 3.4 20.6 - - + +
878B GLY* 3.2 21.1 - - - +
881B MET* 5.6 0.2 - - - -
882B SER* 3.7 11.0 - - - +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL* 3.0 38.1 + - + +
72A HIS 3.8 2.9 - - - +
74A ALA* 1.3 75.2 - - - +
76A ALA* 1.3 64.9 + - - +
78A GLY* 3.0 11.3 + - - -
79A ALA 3.5 17.7 - - - +
80A LEU* 4.6 0.7 - - - -
81A THR* 3.8 17.3 - - - +
100A ILE* 4.1 18.6 - - + -
105A LEU* 3.7 17.2 - - + +
106A PRO* 3.9 17.9 - - + +
107A GLY* 3.6 38.4 - - - +
203A PHE* 3.5 17.9 - - + -
207A SER* 4.1 0.7 + - - -
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Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A HIS* 2.9 18.7 + - + +
73A GLY 3.3 5.4 + - - +
75A LEU* 1.3 77.1 - - - +
77A ALA* 1.3 56.9 - - - +
78A GLY 3.3 0.2 - - - -
105A LEU* 4.0 4.8 - - + +
207A SER* 3.5 5.9 - - - -
208A MET* 2.9 48.4 + - - +
216A ARG* 3.8 30.8 + - - +
875B TYR* 4.1 11.0 - - + +
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLY 3.0 16.6 + - - +
74A ALA 3.4 0.9 - - - -
75A LEU 3.1 0.6 - - - -
76A ALA* 1.3 76.7 - - - +
78A GLY* 1.3 53.3 + - - +
207A SER* 3.8 5.2 - - - -
208A MET* 4.3 10.2 - - + +
833B PHE* 4.3 13.9 - - + -
879B MET* 3.8 23.6 - - + +
882B SER* 2.7 35.2 + - - +
883B MET* 5.4 2.6 - - + +
886B ARG* 2.8 16.1 + - - -
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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