Contacts of the helix formed by residues 160 - 178 (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 SER 160 (chain p).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159p ILE* 1.3 74.5 - - - +
161p ALA* 1.3 60.8 + - - +
162p PHE* 3.2 10.8 - - - -
163p ASP* 3.4 13.0 + - - +
164p LEU* 2.9 30.7 + - - +
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Residues in contact with ALA 161 (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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159p ILE 4.0 0.4 + - - -
160p SER* 1.3 72.9 - - - +
162p PHE* 1.3 62.8 + - - +
164p LEU* 3.6 8.2 - - - +
165p ASP* 3.3 20.4 + - - +
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Residues in contact with PHE 162 (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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160p SER* 3.2 6.9 - - - -
161p ALA* 1.3 74.7 - - - +
163p ASP* 1.3 66.6 + - - +
165p ASP* 3.2 8.6 + - - +
166p VAL* 3.1 20.5 + - - +
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Residues in contact with ASP 163 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159p ILE* 5.0 6.5 - - + -
160p SER* 3.4 18.2 + - - +
162p PHE* 1.3 77.5 - - - +
164p LEU* 1.3 63.3 + - - +
166p VAL* 3.1 9.2 + - - +
167p VAL* 2.8 27.0 + - - +
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Residues in contact with LEU 164 (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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159p ILE* 4.9 10.9 - - + +
160p SER 2.9 19.3 + - - +
161p ALA* 3.6 11.0 - - - +
162p PHE 3.2 0.2 - - - -
163p ASP* 1.3 76.6 - - - +
165p ASP* 1.3 56.3 + - - +
167p VAL* 3.6 5.3 + - - +
168p LYS* 3.1 27.4 + - - +
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Residues in contact with ASP 165 (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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161p ALA 3.3 9.4 + - - +
162p PHE* 3.2 10.1 + - - +
164p LEU* 1.3 76.3 - - - +
166p VAL* 1.3 56.3 + - - +
168p LYS* 3.2 5.8 + - - +
169p LEU* 2.8 37.6 + - - +
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Residues in contact with VAL 166 (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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162p PHE 3.1 13.3 + - - +
163p ASP* 3.1 12.8 + - - +
165p ASP* 1.3 75.4 - - - +
167p VAL* 1.3 61.5 + - - +
169p LEU* 3.6 6.0 - - - +
170p THR* 3.0 26.7 + - - -
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Residues in contact with VAL 167 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163p ASP* 2.8 19.8 + - + +
164p LEU* 3.9 5.6 - - - +
166p VAL* 1.3 75.1 - - - +
168p LYS* 1.3 56.4 + - - +
170p THR* 3.4 5.0 + - - -
171p ALA* 2.8 31.8 + - - +
197p PHE* 6.2 3.8 - - + -
204p LEU* 6.0 4.5 - - + +
207p TYR* 6.4 1.3 - - + -
208p PHE* 5.2 18.1 - - + +
211p LEU* 6.2 0.4 - - - -
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Residues in contact with LYS 168 (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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164p LEU 3.1 18.7 + - - +
165p ASP* 3.2 6.7 + - - +
167p VAL* 1.3 74.0 - - - +
169p LEU* 1.3 52.7 + - - +
171p ALA* 3.1 8.0 + - - +
172p GLN* 2.8 36.3 + - - +
211p LEU* 5.8 3.8 - - - -
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Residues in contact with LEU 169 (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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165p ASP 2.8 22.1 + - - +
166p VAL* 3.6 7.2 - - - +
168p LYS* 1.3 71.7 - - - +
170p THR* 1.3 62.8 + - - +
172p GLN* 3.2 6.8 + - - +
173p PHE* 3.1 22.7 + - - +
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Residues in contact with THR 170 (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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166p VAL 3.0 18.2 + - - -
167p VAL* 3.7 5.2 - - - -
169p LEU* 1.3 75.8 - - - +
171p ALA* 1.3 57.4 + - - +
173p PHE* 3.2 6.7 + - - +
174p VAL* 3.0 31.6 + - - +
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Residues in contact with ALA 171 (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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167p VAL 2.8 22.2 + - - +
168p LYS* 3.5 5.4 - - - +
170p THR* 1.3 71.6 - - - +
172p GLN* 1.3 60.7 + - - +
174p VAL* 4.3 4.4 - - - -
175p ALA* 3.2 24.9 + - - +
208p PHE* 4.1 10.1 - - + +
211p LEU* 3.8 30.5 - - + -
212p VAL* 4.0 15.5 - - - +
215p TYR* 4.0 2.4 - - + +
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Residues in contact with GLN 172 (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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59 LEU* 5.3 10.6 - - + +
69 GLU* 5.1 21.3 - - + +
168p LYS 2.8 16.4 + - - +
169p LEU* 3.5 7.0 - - - +
171p ALA* 1.3 74.8 - - - +
173p PHE* 1.3 64.4 + - - +
175p ALA* 3.3 5.0 + - - +
176p ARG* 3.1 22.4 + - - +
215p TYR* 4.2 13.6 - - + +
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Residues in contact with PHE 173 (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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169p LEU 3.1 15.2 + - - +
170p THR* 3.8 5.2 - - - +
172p GLN* 1.3 73.3 - - - +
174p VAL* 1.3 64.8 + - - +
176p ARG* 3.1 8.8 + - - +
177p ASN* 3.0 26.2 + - - +
181p PHE* 5.7 1.8 - - - -
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Residues in contact with VAL 174 (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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170p THR 3.0 17.2 + - - +
171p ALA* 4.3 5.6 - - - +
173p PHE* 1.3 74.2 - - - +
175p ALA* 1.3 56.5 + - - +
178p GLY* 2.8 39.0 + - - +
179p ARG* 5.9 0.2 - - - -
181p PHE* 5.0 5.2 - - - -
182p LEU* 4.0 28.3 - - + -
212p VAL* 5.5 7.0 - - + -
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Residues in contact with ALA 175 (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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171p ALA 3.2 20.7 + - - +
172p GLN 3.5 3.4 - - - +
173p PHE 3.2 0.2 - - - -
174p VAL* 1.3 76.1 - - - +
176p ARG* 1.3 57.3 + - - +
178p GLY* 4.5 2.3 + - - -
212p VAL* 3.6 11.8 - - - +
215p TYR* 3.4 28.7 - - + +
216p THR* 3.6 27.5 - - - +
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Residues in contact with ARG 176 (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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59 LEU* 5.5 9.6 - - + -
172p GLN 3.1 12.1 + - - +
173p PHE* 3.1 13.3 + - - +
175p ALA* 1.3 79.4 - - - +
177p ASN* 1.3 58.4 + - + +
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Residues in contact with ASN 177 (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 3.0 11.3 + - - +
176p ARG* 1.3 76.1 - - + +
178p GLY* 1.3 60.9 + - - +
180p GLN* 5.2 3.8 + - - +
181p PHE* 3.8 25.0 + - + +
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Residues in contact with GLY 178 (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* 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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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