Contacts of the helix formed by residues 177 - 187 (chain T) in PDB entry 6FF7
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 177 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172T LYS 5.4 5.2 - - - +
173T VAL* 5.9 0.7 - - - -
174T ASN* 3.7 13.3 + - + +
175T ILE 3.2 0.6 - - - -
176T SER* 1.3 80.9 - - - +
178T ILE* 1.3 64.7 + - - +
179T SER* 3.1 3.8 + - - -
180T ILE* 3.1 11.7 + - + +
181T ILE* 3.1 21.0 + - + +
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Residues in contact with ILE 178 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173T VAL* 5.6 2.9 - - + -
174T ASN 3.4 17.7 + - - +
175T ILE* 3.6 10.2 + - - +
176T SER 3.7 0.4 - - - -
177T ASN* 1.3 76.1 - - - +
179T SER* 1.3 56.8 + - - +
181T ILE* 3.2 9.0 + - - +
182T ILE* 2.9 29.9 + - - +
214T VAL* 5.9 2.9 - - + +
217T ALA* 5.9 7.0 - - + -
218T LEU* 6.1 6.5 - - + +
356T GLY 5.5 4.9 - - - +
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Residues in contact with SER 179 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177T ASN 3.1 1.6 + - - -
178T ILE* 1.3 78.8 - - - +
180T ILE* 1.3 62.5 + - - +
182T ILE* 3.3 8.0 + - - +
183T GLN* 3.1 22.0 + - - +
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Residues in contact with ILE 180 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177T ASN* 3.1 13.1 + - + +
179T SER* 1.3 75.4 - - - +
181T ILE* 1.3 66.2 + - - +
183T GLN* 3.2 8.6 + - - +
184T GLU* 2.9 25.4 + - - +
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Residues in contact with ILE 181 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169T LEU* 4.9 15.4 - - + +
172T LYS* 6.0 2.2 - - + -
173T VAL* 4.4 22.2 - - + +
177T ASN* 3.1 13.2 + - + +
178T ILE* 3.5 12.3 - - - +
180T ILE* 1.3 76.7 - - - +
182T ILE* 1.3 57.2 + - - +
184T GLU* 3.2 7.0 + - - +
185T LEU* 2.8 32.4 + - - +
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Residues in contact with ILE 182 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178T ILE 2.9 13.7 + - - +
179T SER* 3.5 10.8 - - - +
181T ILE* 1.3 76.1 - - - +
183T GLN* 1.3 58.3 + - - +
185T LEU* 3.1 7.2 + - - +
186T LEU* 2.9 32.0 + - - +
221T ILE* 5.1 14.8 - - + -
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Residues in contact with GLN 183 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179T SER 3.1 13.4 + - - +
180T ILE* 3.2 11.0 + - - +
182T ILE* 1.3 78.1 - - - +
184T GLU* 1.3 62.1 + - - +
186T LEU* 3.6 7.5 + - - +
187T GLN* 3.5 16.8 + - - +
406T LEU 5.2 4.1 - - - +
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Residues in contact with GLU 184 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169T LEU* 5.9 4.9 - - + -
180T ILE 2.9 15.8 + - - +
181T ILE* 3.8 5.8 - - - +
183T GLN* 1.3 73.7 - - - +
185T LEU* 1.3 66.8 + - - +
187T GLN* 3.3 19.2 + - - +
188T GLU* 3.9 3.8 + - - +
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Residues in contact with LEU 185 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169T LEU* 5.2 12.9 - - + +
181T ILE 2.8 17.7 + - - +
182T ILE* 3.1 8.3 + - - +
184T GLU* 1.3 78.1 - - - +
186T LEU* 1.3 56.7 + - - +
188T GLU* 3.0 30.6 + - - +
190T ILE* 4.8 7.4 - - - +
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Residues in contact with LEU 186 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182T ILE 2.9 16.8 + - - +
183T GLN* 3.9 7.0 - - - +
184T GLU 3.3 0.2 - - - -
185T LEU* 1.3 76.4 - - - +
187T GLN* 1.3 60.9 + - - +
188T GLU 3.3 8.4 + - - +
190T ILE* 6.0 1.3 - - - -
402T LYS* 4.4 16.2 - - + +
406T LEU 4.4 19.7 - - - +
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Residues in contact with GLN 187 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183T GLN 3.5 9.0 + - - +
184T GLU* 3.3 16.0 + - - +
185T LEU 3.1 1.0 - - - -
186T LEU* 1.3 78.3 - - - +
188T GLU* 1.3 60.2 + - - +
189T ASN 4.1 0.3 + - - -
402T LYS* 5.7 3.6 - - - -
406T LEU 5.5 0.4 + - - -
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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