Contacts of the helix formed by residues 165 - 176 (chain O) in PDB entry 5M32
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 165 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29O ALA 5.0 0.4 + - - -
33O PRO* 4.8 4.2 - - - +
163O GLY 3.8 0.8 + - - -
164O LYS* 1.3 91.7 - - + +
166O TYR* 1.3 57.0 + - - +
167O VAL* 3.2 7.4 - - - +
168O ASN* 3.1 43.2 + - - +
169O GLY 3.6 2.3 + - - -
196O GLU* 6.1 2.5 - - - +
197O SER* 3.7 31.8 + - - -
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Residues in contact with TYR 166 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29O ALA* 4.0 24.3 - - + +
161O ALA* 4.0 10.8 - - - +
162O MET* 3.7 32.3 - - - +
163O GLY 3.4 16.8 - - - -
164O LYS 3.0 3.5 + - - -
165O ASN* 1.3 73.6 - - - +
167O VAL* 1.3 73.9 + - + +
168O ASN 3.2 0.4 - - - -
169O GLY* 3.6 3.7 - - - +
170O LYS* 2.9 62.3 + - + +
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Residues in contact with VAL 167 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165O ASN* 3.2 2.4 - - - -
166O TYR* 1.3 99.1 - - + +
168O ASN* 1.3 60.6 + - - +
170O LYS* 3.3 9.3 + - - +
171O THR* 2.8 47.1 + - + +
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Residues in contact with ASN 168 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165O ASN* 3.1 34.7 + - + +
167O VAL* 1.3 81.2 - - - +
169O GLY* 1.3 58.4 + - - +
171O THR* 3.2 8.0 + - - -
172O PHE* 2.9 33.1 + - - +
196O GLU* 3.5 26.5 + - - +
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Residues in contact with GLY 169 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161O ALA* 3.8 23.1 + - - -
165O ASN 3.6 3.6 + - - -
166O TYR 3.2 8.3 + - - -
167O VAL 3.2 0.8 - - - -
168O ASN* 1.3 77.7 - - - +
170O LYS* 1.3 57.8 + - - +
172O PHE* 4.5 0.4 - - - -
173O LEU* 2.9 35.5 + - - +
193O THR* 4.5 15.3 - - - -
196O GLU* 4.7 1.5 + - - -
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Residues in contact with LYS 170 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160O THR* 4.4 21.1 - - - +
161O ALA 4.5 8.7 - - - +
166O TYR* 2.9 49.2 + - + +
167O VAL* 4.0 10.3 - - - +
169O GLY* 1.3 74.1 - - - +
171O THR* 1.3 62.3 + - + +
173O LEU* 3.9 1.5 - - - -
174O GLU* 2.9 29.5 + - - +
53P HIS* 3.7 32.0 + - + +
55P LEU* 3.5 17.9 - - + +
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Residues in contact with THR 171 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167O VAL* 2.8 32.3 + - + +
168O ASN* 3.2 12.6 + - - -
170O LYS* 1.3 78.1 - - + +
172O PHE* 1.3 60.5 + - - +
174O GLU* 3.2 7.0 + - - +
175O LYS* 3.0 26.9 + - - +
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Residues in contact with PHE 172 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168O ASN 2.9 22.4 + - - +
169O GLY* 4.1 1.8 - - - +
171O THR* 1.3 78.0 + - - +
173O LEU* 1.3 61.8 + - + +
175O LYS* 3.3 8.8 + - + +
176O ARG* 3.0 58.6 + - + +
189O THR* 4.2 6.5 - - - -
192O LEU* 3.6 41.1 - - + -
193O THR* 3.7 22.0 - - + -
196O GLU* 4.3 20.2 - - - +
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Residues in contact with LEU 173 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O VAL* 3.9 13.9 - - + -
37O ILE* 3.8 24.5 - - + -
159O ALA* 3.8 33.4 - - + +
160O THR* 4.8 3.6 - - - +
169O GLY 2.9 26.0 + - - +
170O LYS* 4.2 3.4 - - - +
172O PHE* 1.3 79.8 - - + +
174O GLU* 1.3 64.4 + - - +
176O ARG 3.6 17.9 - - - +
177O TYR* 3.3 26.4 - - + +
189O THR* 4.4 7.4 - - + +
193O THR* 3.4 36.1 - - + +
55P LEU* 4.8 5.6 - - + +
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Residues in contact with GLU 174 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170O LYS 2.9 19.8 + - - +
171O THR* 3.2 9.2 + - - +
173O LEU* 1.3 79.6 - - - +
175O LYS* 1.3 61.2 + - - +
177O TYR* 4.6 4.6 + - - +
54P LYS* 5.5 13.5 - - + -
55P LEU* 4.2 18.3 - - + +
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Residues in contact with LYS 175 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171O THR 3.0 12.7 + - - +
172O PHE* 3.5 14.1 - - + +
173O LEU 3.2 0.2 - - - -
174O GLU* 1.3 78.8 - - - +
176O ARG* 1.3 66.4 + - + +
177O TYR 3.4 5.9 + - - +
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Residues in contact with ARG 176 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172O PHE* 3.0 41.1 + - + +
173O LEU* 3.6 18.4 - - - +
175O LYS* 1.3 79.0 - - + +
177O TYR* 1.3 61.6 + - - +
181O LEU* 6.1 0.3 - - - +
188O HIS* 5.7 0.4 + - - -
189O THR* 4.4 17.6 + - - +
192O LEU* 3.4 35.7 - - - +
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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