Contacts of the helix formed by residues 157 - 163 (chain I) in PDB entry 1KN0
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 157 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72H ILE* 3.5 21.1 - - - +
76H ASN* 3.2 19.4 + - - +
84H TRP* 3.7 11.9 - - - -
86H HIS* 3.5 18.5 + - - -
151H LEU* 5.1 2.1 - - - +
121I HIS* 3.4 28.6 - - - +
123I ASP* 4.6 2.9 + - - -
153I ARG 3.9 7.4 + - - -
154I ALA* 3.1 16.4 + - - -
155I LEU 3.0 0.8 - - - -
156I ARG* 1.3 79.6 - - - +
158I PHE* 1.3 58.9 + - - +
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Residues in contact with PHE 158 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76H ASN* 3.3 17.0 - - - +
81H TYR* 3.7 20.8 - + + +
43I LEU* 3.6 26.1 - - + +
79I PHE* 4.3 5.8 - + + -
113I VAL* 4.1 30.5 - - + -
115I LEU* 3.5 41.5 - - + -
119I SER* 4.0 6.1 - - - -
120I TYR* 4.8 1.8 - - - -
121I HIS* 3.1 40.4 - + - -
154I ALA 4.8 2.5 - - - -
155I LEU* 3.0 31.5 + - + +
157I SER* 1.3 79.6 - - - +
159I GLY* 1.3 56.1 + - - +
162I LEU* 3.7 15.9 - - + -
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Residues in contact with GLY 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73H ASN* 4.3 3.8 - - - -
76H ASN* 4.0 10.1 - - - -
43I LEU* 3.8 9.6 - - - +
155I LEU 4.2 0.4 + - - -
156I ARG 3.2 8.4 + - - +
157I SER 3.3 0.8 - - - -
158I PHE* 1.3 82.7 - - - +
160I ASN* 1.3 66.8 + - - -
161I ALA 3.4 2.2 - - - -
162I LEU* 3.2 11.2 + - - +
163I GLY 3.6 0.7 + - - -
164I ASN* 3.1 22.6 + - - +
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Residues in contact with ASN 160 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H HIS* 5.9 0.3 - - - -
73H ASN* 3.1 35.1 + - - +
43I LEU 3.0 4.4 + - - -
44I ARG* 3.1 24.7 + - - +
45I GLN 3.1 18.8 - - - +
46I ARG* 4.5 15.8 + - + +
47I LEU* 2.9 13.7 - - - +
159I GLY* 1.3 67.0 - - - -
161I ALA* 1.3 56.1 + - - +
162I LEU 3.0 5.4 - - - -
163I GLY* 2.8 20.8 + - - -
164I ASN* 3.5 14.7 + - - +
165I CYS* 3.7 23.3 + - + +
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Residues in contact with ALA 161 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192H LYS* 4.5 15.7 - - + -
42I ALA 3.4 25.8 - - - +
43I LEU* 3.0 21.3 + - + +
45I GLN* 3.0 11.8 + - + +
47I LEU* 3.7 12.7 - - - +
74I LEU* 3.1 28.1 - - - +
78I MET* 5.1 7.3 - - + +
159I GLY 3.4 0.4 - - - -
160I ASN* 1.3 73.7 - - - +
162I LEU* 1.3 59.7 + - + +
163I GLY 3.4 0.4 - - - -
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Residues in contact with LEU 162 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I LEU* 3.8 16.8 - - + +
47I LEU* 4.9 0.2 - - - -
66I ILE* 4.9 3.3 - - - +
71I VAL* 4.4 20.1 - - + +
74I LEU* 3.8 33.0 - - + +
75I ALA* 3.8 21.5 - - + +
78I MET* 4.8 3.6 - - + -
79I PHE* 3.8 20.0 - - + -
152I LYS 4.7 0.7 - - - +
155I LEU* 3.4 26.1 - - + +
156I ARG* 3.8 15.2 + - - +
158I PHE* 3.7 28.9 - - + -
159I GLY 3.2 7.8 + - - +
160I ASN 2.9 1.6 + - - -
161I ALA* 1.3 80.0 - - - +
163I GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 163 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47I LEU* 4.0 4.0 - - - +
66I ILE* 3.8 22.7 - - - -
156I ARG* 3.6 12.9 - - - +
160I ASN 2.8 8.8 + - - -
161I ALA 3.4 1.0 - - - -
162I LEU* 1.3 80.6 - - - +
164I ASN* 1.3 56.6 + - - +
165I CYS* 3.0 7.6 + - - -
166I ILE* 3.0 30.2 - - - +
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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