Contacts of the strand formed by residues 154 - 159 (chain F) 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 VAL 154 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F MET* 4.0 9.7 - - - +
127F ALA* 4.5 14.7 - - + +
128F SER 3.4 33.4 + - - +
129F THR* 4.4 2.3 + - - -
131F LYS* 4.3 12.8 - - - +
132F THR 5.1 2.9 - - - +
133F VAL* 5.7 2.7 - - + +
150F HIS* 5.6 3.4 - - + -
152F SER 3.4 3.0 + - - +
153F PHE* 1.3 73.9 - - - +
155F ASN* 1.3 60.8 - - - +
156F SER 4.8 2.9 - - - +
169F THR* 5.5 8.3 - - - -
170F GLY 3.6 8.7 - - - +
171F SER* 4.1 3.4 - - - -
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Residues in contact with ASN 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F MET* 3.6 20.6 - - - +
114F GLU* 4.8 0.5 - - - +
127F ALA* 4.9 0.4 - - - -
153F PHE* 3.5 5.2 + - + +
154F VAL* 1.3 73.0 - - - +
156F SER* 1.3 60.9 + - - +
170F GLY 2.9 9.3 + - - +
171F SER* 4.6 3.4 - - - -
172F ASP 5.3 0.4 - - - +
196F VAL 3.5 25.1 - - - +
197F LEU* 3.9 14.2 - - + +
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Residues in contact with SER 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F GLU* 4.6 7.9 - - - -
127F ALA* 4.3 10.1 - - - +
154F VAL* 3.6 2.8 - - - +
155F ASN* 1.3 82.3 - - - +
157F CYS* 1.3 62.1 + - - +
168F CYS 3.8 0.2 - - - +
169F THR* 3.3 5.9 - - - -
170F GLY* 3.1 28.0 + - - +
197F LEU 3.5 18.4 - - - -
198F ALA* 4.2 11.9 - - - -
199F VAL* 4.5 9.1 - - - +
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Residues in contact with CYS 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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114F GLU* 4.6 11.6 - - + +
116F HIS* 4.8 10.9 - - - +
125F PHE* 5.5 11.4 - - + -
126F SER 5.8 0.2 - - - -
127F ALA* 4.2 19.5 - - + +
133F VAL* 5.3 9.0 - - + -
156F SER* 1.3 78.7 - - - +
158F TYR* 1.3 62.7 + - - +
167F VAL* 6.2 2.7 - - + -
168F CYS 2.9 13.7 - - - +
169F THR* 4.7 4.9 - - - -
199F VAL* 4.6 5.7 - - - +
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Residues in contact with TYR 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F HIS* 5.4 4.5 - - - -
157F CYS* 1.3 76.1 - - - +
159F PRO* 1.3 62.5 - - - +
160F ALA 4.1 0.3 + - - -
167F VAL* 3.4 5.2 - - - +
168F CYS* 2.9 35.4 + - + +
199F VAL 3.4 20.8 + - - +
200F THR* 4.1 13.7 - - - -
201F PHE* 4.6 6.7 - - + +
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Residues in contact with PRO 159 (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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116F HIS* 5.2 10.5 - - + -
117F TYR 4.9 4.5 - - - +
118F ASN* 4.8 21.8 - - + +
125F PHE* 5.4 9.4 - - + -
158F TYR* 1.3 76.8 - - - +
160F ALA* 1.3 66.4 + - - +
161F ARG* 3.4 3.6 + - - +
166F LEU 3.4 9.4 - - - +
167F VAL* 4.6 2.5 - - + -
201F PHE* 5.7 1.8 - - - -
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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