Contacts of the strand formed by residues 130 - 135 (chain F) in PDB entry 6G2T
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 ALA 130 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101F PRO* 3.4 10.6 - - + +
102F VAL 3.2 15.0 + - - -
123F PHE* 4.8 1.3 - - - -
128F THR* 3.2 18.8 + - - -
129F PRO* 1.3 85.5 - - + +
131F MET* 1.3 63.0 + - - +
355F TRP* 3.9 22.2 - - + -
356F ILE 3.2 13.0 - - - +
357F SER* 3.7 14.1 - - - +
358F LYS 4.3 0.9 - - - +
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Residues in contact with MET 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F VAL* 3.1 22.4 - - + +
104F LEU* 3.6 19.1 - - + -
119F THR* 3.7 27.4 - - + +
122F MET* 3.3 40.8 - - + -
123F PHE* 3.3 40.4 - - + -
128F THR* 4.7 1.8 - - + -
130F ALA* 1.3 77.0 - - - +
132F TYR* 1.3 63.2 + - - +
133F VAL* 4.4 8.5 - - + -
355F TRP* 3.4 4.9 - - - -
356F ILE* 2.8 37.6 + - + +
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Residues in contact with TYR 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D VAL* 4.7 14.7 - - - +
102F VAL 3.1 5.7 + - - +
103F LEU* 3.3 18.8 - - + +
104F LEU* 2.9 26.3 + - - +
131F MET* 1.3 79.1 - - - +
133F VAL* 1.3 93.4 + - - +
134F ALA* 3.6 14.3 - - + +
345F LEU* 4.7 1.3 - - + -
351F PHE* 3.5 25.7 - + + -
354F MET* 3.9 36.6 - - + +
355F TRP* 3.3 24.2 - - + -
356F ILE* 4.6 10.8 - - + -
372F LYS* 5.7 1.8 - - + -
373F CYS* 3.6 27.3 - - + +
374F PHE* 4.9 0.5 + - - -
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Residues in contact with VAL 133 (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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104F LEU* 3.3 21.1 - - + +
106F GLU* 4.8 14.8 - - + -
115F ARG* 5.1 9.4 - - + +
118F MET* 4.5 13.0 - - + -
119F THR* 4.3 17.9 - - + -
131F MET* 4.4 4.9 - - + -
132F TYR* 1.3 97.5 + - - +
134F ALA* 1.3 60.6 + - - +
356F ILE* 4.8 5.8 - - + -
369F VAL* 3.7 19.1 - - + -
373F CYS* 3.4 28.9 - - - -
374F PHE* 4.1 5.6 - - - +
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Residues in contact with ALA 134 (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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103F LEU* 4.4 3.8 - - + -
104F LEU 3.0 9.9 + - - +
105F THR* 3.4 3.5 - - - -
106F GLU* 2.6 37.1 + - - -
132F TYR* 3.6 19.5 - - + +
133F VAL* 1.3 76.6 - - - +
135F ILE* 1.3 57.2 + - - +
138F VAL* 6.3 0.4 - - + -
139F LEU* 3.4 24.0 - - + -
345F LEU* 4.3 10.1 - - + -
374F PHE* 5.1 3.1 - - - -
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Residues in contact with ILE 135 (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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42D VAL* 5.5 5.7 - - + +
106F GLU* 3.1 19.3 - - + +
107F ALA 3.4 5.8 - - - +
108F PRO* 3.2 43.1 - - + -
115F ARG* 4.1 11.4 - - - +
134F ALA* 1.3 74.2 - - - +
136F GLN* 1.3 63.1 + - - +
137F ALA* 4.3 5.8 - - + +
138F VAL* 3.3 37.9 + - + +
139F LEU* 2.9 20.5 - - - +
162F VAL* 5.1 4.7 - - + -
174F ILE* 6.4 0.7 - - + -
374F PHE* 4.7 33.1 + - + +
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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