Contacts of the strand formed by residues 123 - 128 (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 MET 123 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F TYR* 3.5 5.4 - - - +
118F ASN* 3.0 42.6 + - + +
121F GLY 3.6 0.6 - - - -
122F SER* 1.3 83.4 + - - +
124F LEU* 1.3 61.3 + - - +
125F PHE 4.2 0.4 + - - -
135F VAL* 6.0 4.0 - - + -
136F TRP 3.4 7.0 - - - +
138F SER* 5.1 2.2 - - - -
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Residues in contact with LEU 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F LEU* 6.5 1.1 - - + -
116F HIS 3.3 7.9 - - - +
117F TYR* 4.6 2.5 - - + +
123F MET* 1.3 75.3 - - - +
125F PHE* 1.3 62.4 + - - +
126F SER* 5.2 0.7 - - - -
134F ALA 3.8 0.7 - - - +
135F VAL* 3.7 1.1 - - - -
136F TRP* 2.8 54.1 + - + +
138F SER* 5.0 11.9 - - - +
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Residues in contact with PHE 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F GLU 3.4 1.6 - - - +
115F LEU* 3.2 8.3 - - - +
116F HIS* 2.9 42.1 + - + +
123F MET 4.2 0.8 - - - -
124F LEU* 1.3 73.9 - - - +
126F SER* 1.3 62.7 + - - +
127F ALA 4.2 0.2 - - - -
133F VAL* 6.4 1.1 - - + -
134F ALA 3.4 7.0 - - - +
135F VAL* 4.8 2.5 - - + +
157F CYS* 5.5 11.2 - - + -
158F TYR 6.3 1.3 - - - -
159F PRO* 5.4 10.3 - - + -
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Residues in contact with SER 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F VAL* 5.5 9.2 - - - -
114F GLU 3.3 5.6 - - - -
115F LEU* 5.4 2.0 - - - -
124F LEU 5.2 1.6 - - - -
125F PHE* 1.3 75.8 - - - +
127F ALA* 1.3 63.4 + - - +
128F SER* 3.6 3.0 + - - -
132F THR 3.8 0.9 - - - +
133F VAL* 3.4 5.4 - - - +
134F ALA* 2.9 45.0 + - - +
136F TRP* 6.2 2.5 - - - -
157F CYS* 5.8 0.4 - - - -
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Residues in contact with ALA 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F VAL* 3.7 3.2 - - - -
113F MET* 2.8 35.3 + - + +
114F GLU* 3.0 20.9 + - + +
125F PHE 4.2 0.4 - - - -
126F SER* 1.3 72.1 - - - +
128F SER* 1.3 53.6 + - - +
132F THR 4.3 2.2 - - - -
133F VAL* 4.5 6.5 - - + +
154F VAL* 4.5 12.1 - - + -
156F SER* 4.3 10.3 - - - +
157F CYS* 4.2 31.0 - - + +
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Residues in contact with SER 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F HIS* 4.6 14.8 - - - -
109F SER 5.7 0.2 - - - -
110F GLY* 4.5 8.1 - - - -
111F ALA 3.2 13.2 - - - -
112F VAL* 4.9 1.1 - - - -
113F MET* 5.2 0.7 - - - -
126F SER* 3.6 2.7 + - - -
127F ALA* 1.3 75.2 - - - +
129F THR* 1.3 63.7 + - - +
130F ASP* 3.1 13.7 + - - -
131F LYS* 3.3 10.4 + - - -
132F THR* 3.3 20.0 + - - -
154F VAL* 3.4 22.3 + - - +
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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