Contacts of the helix formed by residues 67 - 77 (chain A) 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 GLY 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A GLU* 2.7 14.3 + - - -
66A ASN* 1.3 75.6 + - - +
68A VAL* 1.3 64.6 + - - +
69A SER 3.0 2.2 - - - -
70A ASN* 3.2 4.3 + - - +
71A LEU* 3.1 28.8 + - - +
177A THR 4.1 5.2 - - - -
178A ARG 3.9 4.0 - - - -
179A GLY* 3.5 17.7 - - - -
184A LEU* 3.6 9.3 - - - +
187A LEU* 4.1 1.3 - - - -
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Residues in contact with VAL 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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61A GLU* 3.3 15.2 + - + +
65A ASN* 3.0 23.8 + - + +
67A GLY* 1.3 78.1 - - - +
69A SER* 1.3 66.3 + - - +
71A LEU* 3.3 6.6 - - - +
72A TRP* 3.1 26.1 + - - -
187A LEU* 3.5 15.2 - - + +
191A ASP* 4.0 13.9 - - + +
192A LEU* 3.8 21.3 - - + +
195A PHE* 3.7 46.7 - - + -
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Residues in contact with SER 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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57A GLY 4.4 4.0 - - - -
61A GLU* 2.8 18.1 + - - +
67A GLY 3.0 0.6 - - - -
68A VAL* 1.3 82.8 - - - +
70A ASN* 1.3 64.6 + - - +
71A LEU 3.0 1.8 - - - -
72A TRP* 3.1 8.6 + - - +
73A LYS 2.9 20.1 + - - -
96A ILE* 3.1 30.7 - - - +
101A GLN* 3.2 29.4 + - - -
177A THR 5.5 0.2 - - - -
195A PHE* 3.8 7.8 - - - -
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Residues in contact with ASN 70 (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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67A GLY* 3.2 8.5 + - - +
69A SER* 1.3 78.1 - - - +
71A LEU* 1.3 55.4 + - - +
73A LYS* 3.6 10.7 + - - +
74A ASN* 3.0 39.2 + - - +
96A ILE* 4.0 11.6 - - + +
143A VAL* 4.1 16.7 - - + +
146A GLN* 4.1 9.8 + - - +
147A VAL* 3.6 17.8 - - - +
177A THR 4.0 6.1 + - - +
178A ARG* 3.3 47.5 + - - +
184A LEU* 5.0 1.3 - - + +
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Residues in contact with LEU 71 (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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67A GLY 3.1 18.5 + - - +
68A VAL* 3.3 12.8 - - - +
70A ASN* 1.3 75.3 - - + +
72A TRP* 1.3 59.5 + - - +
74A ASN* 3.1 4.9 + - - +
75A ILE* 2.9 35.9 + - + +
136A PHE* 4.5 15.5 - - + -
139A THR* 3.8 27.6 - - + +
140A LYS* 4.3 11.7 - - + +
143A VAL* 3.7 28.5 - - + -
184A LEU* 4.0 19.1 - - + +
187A LEU* 4.3 10.8 - - + -
192A LEU* 4.0 21.1 - - + -
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Residues in contact with TRP 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 VAL* 3.1 13.9 + - + -
69A SER* 3.1 7.6 + - - +
71A LEU* 1.3 77.7 - - - +
73A LYS* 1.3 61.9 + - - +
75A ILE* 3.2 34.6 - - + +
76A PHE* 3.1 25.3 + - + +
103A TYR* 3.1 22.8 - + - +
123A PHE* 5.8 0.4 - + - -
127A LYS* 3.1 39.9 - - + -
130A LEU* 5.9 3.1 - - + -
131A LEU* 3.4 26.7 - - + -
192A LEU* 3.0 57.3 + - + +
193A GLU* 4.3 2.0 - - - -
195A PHE* 4.1 14.5 - + - -
196A ALA* 3.5 19.8 - - + +
200A PHE* 3.8 20.0 - + + -
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Residues in contact with LYS 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 SER 2.9 16.1 + - - +
70A ASN* 3.7 14.4 - - - +
72A TRP* 1.3 77.4 - - - +
74A ASN* 1.3 66.6 + - - +
76A PHE* 3.3 3.3 + - - +
77A LEU* 3.2 44.2 + - + +
94A SER* 3.0 49.9 + - - +
95A ASN* 3.7 14.5 - - - +
96A ILE* 3.7 25.8 - - + +
103A TYR* 3.8 5.1 + - - -
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Residues in contact with ASN 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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70A ASN* 3.0 31.3 + - - +
71A LEU 3.1 4.0 + - - +
73A LYS* 1.3 84.3 - - - +
75A ILE* 1.3 62.9 + - - +
77A LEU* 3.6 9.3 + - - +
78A SER* 3.3 16.6 + - - -
139A THR* 3.7 12.9 + - + +
142A SER* 3.7 11.4 + - - -
143A VAL* 3.2 29.4 - - + +
146A GLN* 3.6 27.7 + - - +
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Residues in contact with ILE 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 LEU* 2.9 14.6 + - + +
72A TRP* 3.2 55.0 - - + +
74A ASN* 1.3 73.5 - - - +
76A PHE* 1.3 62.8 + - - +
77A LEU 3.2 0.7 - - - -
78A SER* 2.9 27.7 - - - -
81A ASN* 4.2 5.5 - - - +
130A LEU* 4.2 28.8 - - + +
131A LEU* 4.0 16.6 - - + -
135A ASN* 4.9 3.4 - - - +
136A PHE* 4.7 14.4 - - + -
139A THR* 3.3 31.2 - - + +
192A LEU* 4.2 7.0 - - + -
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Residues in contact with PHE 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 TRP* 3.1 19.4 + - + +
73A LYS 3.4 4.9 - - - +
75A ILE* 1.3 79.7 - - + +
77A LEU* 1.3 71.8 + - + +
78A SER 3.2 2.4 + - - -
81A ASN* 3.0 29.6 + - - +
92A LEU* 3.7 39.2 - - + +
93A SER 4.6 1.6 - - - -
94A SER* 4.4 1.8 - - - -
103A TYR* 3.5 39.7 - + + -
104A ILE 4.5 7.4 - - - -
105A VAL* 4.5 2.2 - - + -
118A PHE* 4.7 2.5 - + - -
119A LEU* 4.4 13.7 - - + -
122A SER* 4.5 14.6 - - - -
123A PHE* 3.5 31.2 - + - -
127A LYS* 5.6 4.3 - - - -
130A LEU* 5.3 5.6 - - + -
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Residues in contact with LEU 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 LYS* 3.2 43.8 + - + +
74A ASN* 3.6 11.2 + - - +
75A ILE 3.2 0.2 - - - -
76A PHE* 1.3 92.4 - - + +
78A SER* 1.3 65.5 + - - +
79A LYS* 3.8 0.9 + - - -
82A SER* 3.3 14.4 + - - +
92A LEU* 3.6 33.4 - - + +
93A SER* 4.1 0.4 - - - -
94A SER* 3.9 13.5 - - - +
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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