Contacts of the strand formed by residues 112 - 117 (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 112 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F TYR* 3.8 18.0 - - - +
71F CYS* 5.3 0.7 + - - +
84F ALA* 3.7 30.7 - - + +
85F GLY* 3.1 20.2 + - - +
88F ARG* 4.8 7.0 - - - +
108F HIS* 5.8 4.9 - - + +
110F GLY 3.9 1.2 + - - -
111F ALA* 1.3 70.4 - - - +
113F MET* 1.3 62.4 + - - +
114F GLU 4.9 4.3 - - - +
126F SER* 5.5 9.6 - - - -
127F ALA 3.7 7.2 - - - +
128F SER* 4.6 2.7 - - - +
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Residues in contact with MET 113 (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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70F TYR* 4.4 9.7 - - - +
71F CYS* 4.2 12.2 - - - +
111F ALA* 3.3 5.1 + - - +
112F VAL* 1.3 72.9 - - - +
114F GLU* 1.3 59.0 + - - +
127F ALA* 2.8 16.3 + - + +
128F SER* 5.0 1.1 - - - -
129F THR* 5.3 1.1 - - - +
154F VAL 4.0 12.6 - - - +
155F ASN* 3.6 23.1 - - - +
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Residues in contact with GLU 114 (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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71F CYS* 4.4 5.2 - - + -
112F VAL* 3.6 4.3 - - - +
113F MET* 1.3 84.5 - - - +
115F LEU* 1.3 63.6 + - - +
125F PHE 3.4 1.7 - - - +
126F SER* 3.3 6.7 - - - -
127F ALA* 3.0 38.2 + - + +
155F ASN 4.8 0.7 - - - +
156F SER* 4.6 8.3 - - - -
157F CYS* 4.6 18.6 - - + +
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Residues in contact with LEU 115 (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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71F CYS* 4.2 18.4 - - + +
72F CYS 5.5 0.7 - - - +
73F LYS* 4.7 19.1 - - + +
82F ALA* 5.2 14.6 - - + +
83F SER 6.1 0.2 - - - -
84F ALA* 5.6 10.3 - - + +
114F GLU* 1.3 77.6 - - - +
116F HIS* 1.3 64.5 + - - +
124F LEU* 6.5 1.1 - - + -
125F PHE 3.2 7.4 - - - +
126F SER* 4.8 2.5 - - - +
157F CYS 6.0 0.2 - - - -
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Residues in contact with HIS 116 (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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73F LYS* 5.1 6.1 - - - -
115F LEU* 1.3 78.2 - - - +
117F TYR* 1.3 66.2 + - - +
124F LEU* 3.3 6.9 - - - +
125F PHE* 2.9 40.8 + - + +
157F CYS 4.8 13.5 - - - +
158F TYR* 5.4 0.7 - - - -
159F PRO* 5.2 12.6 - - + -
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Residues in contact with TYR 117 (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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73F LYS* 5.2 7.2 - - + +
74F PHE 4.9 12.6 - - - +
75F HIS* 5.2 3.8 - - - -
76F PRO* 5.0 7.6 - - + -
116F HIS* 1.3 80.5 - - - +
118F ASN* 1.3 72.5 + - - +
121F GLY* 4.7 10.5 - - - -
123F MET 3.5 7.0 - - - +
124F LEU* 4.6 2.5 - - + +
125F PHE* 6.4 0.2 - - - -
159F PRO* 4.9 6.0 - - - +
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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