Contacts of the helix formed by residues 170 - 181 (chain H) in PDB entry 4KYI
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 ASN 170 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161H MET* 4.0 22.4 - - + +
162H GLU* 3.0 32.8 + - - +
163H THR* 3.7 4.1 - - + +
168H ALA 3.3 2.8 + - - -
169H MET* 1.3 82.5 - - - +
171H VAL* 1.3 57.1 + - - +
173H GLU* 3.2 30.8 + - - +
174H ILE* 3.1 28.9 + - - +
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Residues in contact with VAL 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H LEU* 3.8 36.8 - - + +
40H ARG* 3.7 21.8 - - + -
41H PHE* 4.3 8.7 - - + +
163H THR* 4.3 2.5 - - - -
164H SER 3.5 28.7 - - - +
165H ALA* 4.1 2.5 - - - +
168H ALA* 3.5 16.9 + - + +
169H MET 2.8 14.3 + - - +
170H ASN* 1.3 76.7 - - - +
172H ASN* 1.3 65.9 + - + +
174H ILE* 3.3 12.6 - - - +
175H PHE* 3.2 26.4 - - + -
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Residues in contact with ASN 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H PHE* 3.8 32.1 - - + +
63H VAL* 5.4 2.6 - - - +
168H ALA 4.5 2.5 + - - +
171H VAL* 1.3 77.5 - - + +
173H GLU* 1.3 72.2 + - - +
175H PHE* 3.6 2.1 + - - +
176H MET* 3.2 33.3 + - - +
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Residues in contact with GLU 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161H MET* 3.9 18.4 - - + +
168H ALA 4.3 3.3 - - - +
170H ASN* 3.2 40.4 + - - +
171H VAL 3.2 1.8 + - - -
172H ASN* 1.3 84.4 + - - +
174H ILE* 1.3 57.3 + - - +
176H MET* 3.2 6.9 + - - +
177H ALA* 3.0 28.1 + - - +
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Residues in contact with ILE 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H LEU* 6.2 3.8 - - + -
98H ILE* 4.6 12.1 - - + -
130H ALA* 4.6 13.5 - - + -
131H LEU 3.9 20.9 - - - +
132H ALA* 3.9 19.1 - - + -
159H LEU* 4.3 12.1 - - + -
161H MET* 3.7 30.7 - - + +
163H THR* 4.2 7.2 - - + -
170H ASN 3.1 16.1 + - - +
171H VAL* 3.3 16.8 - - - +
173H GLU* 1.3 76.0 - - - +
175H PHE* 1.3 72.7 + - + +
176H MET 3.2 0.6 + - - -
177H ALA* 3.9 2.5 - - - +
178H ILE* 3.1 31.3 + - + +
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Residues in contact with PHE 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H LEU* 4.2 25.6 - - + -
26H LEU* 4.6 13.0 - - + -
37H LEU* 4.4 12.8 - - + -
38H VAL* 4.9 10.5 - - + -
41H PHE* 3.5 65.7 - + + -
72H PHE* 3.4 31.3 - + + -
74H ILE* 4.8 6.7 - - + -
98H ILE* 3.5 28.5 - - + -
171H VAL* 3.2 25.1 + - + -
172H ASN 3.6 3.3 + - - +
173H GLU 3.3 0.6 - - - -
174H ILE* 1.3 86.8 - - + +
176H MET* 1.3 62.4 + - - +
177H ALA 3.6 0.2 - - - -
178H ILE* 4.1 4.2 + - - +
179H ALA* 3.8 4.0 + - - +
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Residues in contact with MET 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F ASP* 5.3 4.3 - - + +
41H PHE* 5.4 0.7 - - - -
63H VAL* 3.6 38.4 - - + -
64H CYS 3.3 29.8 - - - +
65H LEU* 4.4 18.5 - - + +
172H ASN* 3.2 28.7 - - - +
173H GLU* 3.2 8.9 + - - +
175H PHE* 1.3 80.3 - - + +
177H ALA* 1.3 60.7 + - - +
178H ILE 3.1 2.0 - - - -
179H ALA* 3.0 20.1 + - + +
180H LYS* 3.2 28.0 + - - +
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Residues in contact with ALA 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H LEU* 3.3 39.9 - - + +
161H MET* 4.2 12.1 - - + -
173H GLU 3.0 15.3 + - - +
174H ILE 4.1 3.1 - - - +
175H PHE 3.6 0.2 - - - -
176H MET* 1.3 77.9 - - - +
178H ILE* 1.3 60.0 + - - +
180H LYS* 3.7 13.5 + - + +
181H LYS* 3.5 17.0 + - - +
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Residues in contact with ILE 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H LEU* 4.5 9.9 - - + -
72H PHE* 5.0 3.8 - - + -
96H ALA* 3.7 27.4 - - + -
97H ALA 4.6 3.8 - - - +
98H ILE* 3.7 34.5 - - + -
128H VAL* 4.0 17.7 - - + +
130H ALA* 3.9 23.1 - - + -
159H LEU* 4.3 8.3 - - + -
174H ILE* 3.1 19.3 + - + +
175H PHE* 4.2 7.4 - - - +
176H MET 3.1 0.2 - - - -
177H ALA* 1.3 78.1 - - - +
179H ALA* 1.3 64.0 + - - +
180H LYS 3.2 0.7 - - - -
181H LYS* 3.2 10.1 + - - +
182H LEU* 3.2 19.4 + - + +
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Residues in contact with ALA 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H LEU* 3.4 25.1 - - + +
70H VAL* 4.1 28.6 - - + +
72H PHE* 4.2 5.8 - - + -
175H PHE 3.8 9.0 + - - +
176H MET* 3.0 20.7 + - + +
178H ILE* 1.3 80.6 - - - +
180H LYS* 1.3 60.3 + - - +
182H LEU* 3.6 24.9 + - - +
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Residues in contact with LYS 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F ASP* 4.5 10.7 + - - -
65H LEU* 3.7 32.0 - - + +
176H MET* 3.2 23.0 + - - +
177H ALA* 3.9 13.2 - - - +
178H ILE 3.2 0.6 - - - -
179H ALA* 1.3 74.3 - - - +
181H LYS* 1.3 65.8 + - + +
182H LEU 3.1 12.7 + - - -
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Residues in contact with LYS 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H ASN* 5.9 1.2 + - - -
128H VAL* 3.5 29.3 - - + +
159H LEU* 4.1 15.3 - - + -
177H ALA 3.5 15.0 - - - +
178H ILE 3.2 11.1 + - - +
180H LYS* 1.3 80.7 - - - +
182H LEU* 1.3 59.0 + - - +
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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