Contacts of the helix formed by residues 178 - 189 (chain p) 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 GLY 178 (chain p).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174p VAL* 2.8 25.7 + - - +
175p ALA 4.5 2.1 + - - -
176p ARG 3.8 1.0 - - - +
177p ASN* 1.3 72.6 - - - +
179p ARG* 1.3 66.5 + - - +
180p GLN 3.2 3.4 - - - -
181p PHE* 3.1 19.1 + - - +
182p LEU 3.6 2.9 + - - -
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Residues in contact with ARG 179 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174p VAL* 5.9 0.4 - - - -
178p GLY* 1.3 70.2 - - - -
180p GLN* 1.3 63.0 + - - +
182p LEU* 2.9 12.7 + - + +
183p THR* 2.9 24.7 + - - -
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Residues in contact with GLN 180 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177p ASN 5.3 3.6 - - - +
178p GLY 3.1 2.1 + - - +
179p ARG* 1.3 76.4 - - - +
181p PHE* 1.3 62.2 + - - +
183p THR* 3.3 7.3 + - - -
184p GLN* 3.0 22.3 + - - +
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Residues in contact with PHE 181 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173p PHE 5.2 0.7 - - - +
174p VAL* 5.0 6.3 - - - -
177p ASN* 3.8 26.6 + - + +
178p GLY 3.1 11.5 + - - +
180p GLN* 1.3 77.8 - - - +
182p LEU* 1.3 63.1 + - - +
184p GLN* 3.3 16.1 + - - +
185p LEU* 3.3 11.4 + - - +
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Residues in contact with LEU 182 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174p VAL* 4.0 24.5 - - + +
178p GLY 3.6 1.4 + - - -
179p ARG* 2.9 17.6 + - + +
181p PHE* 1.3 75.1 - - - +
183p THR* 1.3 65.9 + - - +
185p LEU* 3.0 19.7 + - - +
186p MET* 3.1 12.1 + - - +
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Residues in contact with THR 183 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179p ARG 2.9 15.3 + - - -
180p GLN* 3.6 11.0 - - - -
182p LEU* 1.3 72.0 - - - +
184p GLN* 1.3 61.8 + - - +
186p MET* 3.2 19.4 + - - +
187p GLN* 3.3 12.5 + - - +
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Residues in contact with GLN 184 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180p GLN 3.0 13.1 + - - +
181p PHE* 3.5 11.9 - - - +
182p LEU 3.2 0.4 - - - -
183p THR* 1.3 75.4 - - - +
185p LEU* 1.3 60.9 + - - +
187p GLN* 3.0 16.6 + - - +
188p LYS* 3.1 15.7 + - - +
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Residues in contact with LEU 185 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181p PHE 3.3 6.9 + - - +
182p LEU* 3.0 12.8 + - - +
184p GLN* 1.3 76.3 - - - +
186p MET* 1.3 62.2 + - - +
188p LYS* 4.7 3.8 - - - +
189p GLU* 3.0 33.4 + - + +
195p PHE* 5.2 5.4 - - + +
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Residues in contact with MET 186 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182p LEU 3.1 11.0 + - - +
183p THR* 3.4 16.2 - - - +
185p LEU* 1.3 74.4 - - - +
187p GLN* 1.3 56.0 + - - +
189p GLU 5.5 0.4 - - - -
190p GLN* 3.4 23.0 - - - +
195p PHE* 5.9 2.5 - - - -
198p LEU* 5.0 17.7 - - + +
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Residues in contact with GLN 187 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183p THR 3.3 8.5 + - - +
184p GLN* 3.0 12.6 + - - +
186p MET* 1.3 76.8 - - - +
188p LYS* 1.3 66.7 + - - +
189p GLU 3.3 0.2 - - - -
190p GLN* 3.3 18.0 + - - +
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Residues in contact with LYS 188 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184p GLN 3.1 11.7 + - - +
185p LEU* 4.5 2.9 - - - +
187p GLN* 1.3 78.4 - - - +
189p GLU* 1.3 58.7 + - + +
190p GLN 3.8 0.3 + - - -
191p ARG 5.3 0.5 + - - -
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Residues in contact with GLU 189 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185p LEU* 3.0 18.1 + - + +
186p MET* 5.0 0.4 - - - -
188p LYS* 1.3 74.7 - - + +
190p GLN* 1.3 65.4 + - - +
191p ARG 3.2 3.4 - - - -
192p ASN* 2.9 32.6 + - + +
195p PHE* 3.7 24.2 - - + +
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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