Contacts of the helix formed by residues 156 - 166 (chain F) in PDB entry 6XAV
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 ASP 156 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147F MET 4.0 1.6 - - - +
148F GLU* 3.8 30.7 - - - +
155F GLU* 1.3 78.5 + - - +
157F LEU* 1.3 64.4 + - + +
158F THR 3.3 0.4 - - - -
159F ALA* 3.3 18.9 + - - +
160F ARG* 3.1 29.0 + - - +
194F SER* 4.9 2.3 + - - -
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Residues in contact with LEU 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F GLU 3.2 6.0 - - - +
156F ASP* 1.3 81.7 - - + +
158F THR* 1.3 62.8 + - - +
160F ARG* 3.4 27.3 + - - +
161F VAL* 3.2 30.3 + - + +
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Residues in contact with THR 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F GLU* 3.7 2.1 + - - -
156F ASP 3.3 0.4 - - - -
157F LEU* 1.3 80.2 - - - +
159F ALA* 1.3 57.0 + - - +
161F VAL* 3.4 6.9 + - + +
162F LEU* 3.0 30.0 + - + +
187F LEU* 3.8 38.5 - - + +
190F ASN* 3.0 35.8 + - + +
191F ILE* 5.7 2.9 - - + -
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Residues in contact with ALA 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F MET* 3.3 36.6 - - + +
155F GLU 4.3 2.5 + - - +
156F ASP* 3.3 18.6 + - - +
158F THR* 1.3 79.7 - - - +
160F ARG* 1.3 58.0 + - - +
162F LEU* 3.4 8.0 + - - +
163F ASP* 3.0 36.0 + - - +
190F ASN* 5.1 4.4 - - + +
191F ILE* 6.3 2.9 - - + -
194F SER* 3.8 11.0 - - - +
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Residues in contact with ARG 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F GLU* 4.2 35.5 + - + -
156F ASP* 3.1 26.9 + - - +
157F LEU* 3.7 25.0 - - + +
158F THR 3.3 0.4 - - - -
159F ALA* 1.3 75.0 - - - +
161F VAL* 1.3 67.3 + - + +
163F ASP* 3.3 7.6 + - - +
164F LEU* 3.0 35.8 + - + +
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Residues in contact with VAL 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F LEU* 3.2 19.5 + - + +
158F THR* 3.9 5.4 - - - +
159F ALA 3.4 0.2 - - - -
160F ARG* 1.3 76.3 - - + +
162F LEU* 1.3 58.8 + - - +
164F LEU* 3.4 8.8 + - + +
165F ALA* 2.9 33.1 + - + +
343F LEU* 6.1 3.1 - - + -
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Residues in contact with LEU 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F MET* 3.7 26.7 - - + -
158F THR* 3.0 19.0 + - + +
159F ALA* 3.7 6.1 - - - +
160F ARG 3.2 0.2 - - - -
161F VAL* 1.3 78.3 - - - +
163F ASP* 1.3 61.0 + - - +
165F ALA* 4.6 3.6 - - - -
166F SER* 2.9 38.9 + - - +
168F ILE* 3.7 33.0 - - + -
176F ILE* 4.5 4.9 - - + -
187F LEU* 5.2 5.4 - - + -
191F ILE* 3.8 31.9 - - + -
343F LEU* 3.8 28.5 - - + -
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Residues in contact with ASP 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F ARG* 3.4 25.7 + - - +
145F LEU 4.7 0.7 - - - +
146F ARG* 4.2 5.1 + - + +
147F MET* 3.3 28.7 + - - +
148F GLU* 3.1 34.6 + - + +
159F ALA 3.0 21.6 + - - +
160F ARG* 3.8 5.3 - - - +
162F LEU* 1.3 80.0 - - - +
164F LEU* 1.3 66.7 + - + +
166F SER 4.4 2.5 - - - -
167F PRO* 3.5 24.8 - - - +
168F ILE 5.0 3.1 + - - -
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Residues in contact with LEU 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F ARG* 3.0 29.8 + - + +
161F VAL* 4.0 7.6 - - + +
163F ASP* 1.3 81.0 - - + +
165F ALA* 1.3 61.7 + - - +
167F PRO* 5.1 2.0 - - - +
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Residues in contact with ALA 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161F VAL* 2.9 22.9 + - + +
162F LEU 4.0 1.3 - - - +
164F LEU* 1.3 80.6 - - - +
166F SER* 1.3 60.5 + - - +
167F PRO* 4.1 4.0 - - - +
343F LEU* 3.8 26.0 - - + -
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Residues in contact with SER 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162F LEU* 2.9 24.6 + - - +
165F ALA* 1.3 75.4 - - - +
167F PRO* 1.3 70.1 - - - +
168F ILE* 3.3 12.3 + - - +
176F ILE* 5.9 0.3 - - - +
341F MET* 3.5 36.1 - - - +
342F GLU 5.5 4.0 - - - -
343F LEU* 4.5 19.9 - - - +
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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