Contacts of the strand formed by residues 131 - 138 (chain H) in PDB entry 2F4V
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 GLY 131 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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598A U 4.3 11.7 - - - -
599A C 4.5 1.8 - - - -
642A A 4.9 3.4 - - - -
94H TYR* 3.3 8.4 - - - -
95H VAL* 2.7 44.2 + - - +
112H LEU* 4.7 6.1 - - - +
113H SER 3.5 10.3 - - - -
114H THR* 4.2 3.2 - - - +
130H GLY* 1.4 73.3 - - - -
132H GLU* 1.3 63.2 + - - -
133H LEU 3.6 0.3 + - - -
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Residues in contact with GLU 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642A A 4.6 2.9 - - + -
643A C 3.2 40.2 + - - +
644A G 4.6 0.7 - - - +
31H PHE* 6.0 1.2 - - - -
85H ARG* 4.1 9.4 + - - -
87H SER* 3.3 34.7 + - - +
92H ARG* 3.9 10.7 + - - -
93H VAL 3.3 10.3 - - - +
94H TYR* 3.3 32.7 + - + -
112H LEU* 3.2 5.4 - - - -
113H SER* 3.0 38.4 + - - +
131H GLY* 1.3 72.0 - - - -
133H LEU* 1.3 62.7 + - - +
134H ILE* 3.3 6.3 + - + +
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Residues in contact with LEU 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86H ILE* 3.5 31.6 - - + -
87H SER* 3.0 29.1 + - - -
93H VAL* 3.2 20.1 + - + +
95H VAL* 4.3 21.9 - - + +
101H PRO* 4.0 25.6 - - + -
110H ALA* 3.9 16.4 - - + -
111H ILE 3.9 3.6 - - - +
112H LEU* 4.6 8.0 - - + +
131H GLY 3.6 3.8 + - - -
132H GLU* 1.3 68.2 - - - +
134H ILE* 1.3 64.9 + - - +
135H CYS 3.7 19.5 - - - +
136H GLU* 5.4 2.2 - - + -
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Residues in contact with ILE 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H ILE* 3.8 26.0 - - + -
31H PHE* 4.1 20.2 - - + -
35H ILE* 4.8 7.0 - - + -
85H ARG* 3.4 19.5 + - - +
86H ILE* 2.7 30.8 + - - +
111H ILE* 2.8 26.7 + - + +
112H LEU 3.4 6.3 - - - -
113H SER* 3.0 44.2 - - - +
118H VAL* 4.8 0.4 - - + -
132H GLU* 3.3 10.1 + - + +
133H LEU* 1.3 74.0 - - - +
135H CYS* 1.3 72.0 + - + +
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Residues in contact with CYS 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H LEU* 3.8 26.2 - - + -
35H ILE* 5.0 2.5 - - - -
39H LEU* 6.4 0.4 - - - -
84H ARG 3.2 17.5 - - - +
86H ILE* 4.0 4.5 - - - -
110H ALA* 3.3 4.5 - - - -
111H ILE* 2.8 47.3 + - - +
133H LEU* 3.7 4.9 - - - +
134H ILE* 1.3 96.0 - - + +
136H GLU* 1.3 66.0 + - - +
137H VAL* 3.9 17.3 - - + -
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Residues in contact with GLU 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82H HIS* 2.9 30.7 + - - -
84H ARG* 2.6 60.5 + - - +
86H ILE* 4.0 14.5 - - + +
101H PRO* 6.2 2.2 - - + -
103H VAL* 4.7 13.3 - - + +
109H ILE 3.5 10.3 - - - +
110H ALA* 5.3 2.9 - - + -
133H LEU* 5.4 1.8 - - + -
135H CYS* 1.3 84.6 - - - +
137H VAL* 1.3 58.8 + - - +
138H TRP* 4.2 10.5 + - - -
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Residues in contact with VAL 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H LEU* 4.4 15.7 - - + -
44H PHE* 3.4 30.8 - - + -
80H ILE* 4.5 7.4 - - + -
82H HIS 3.3 14.8 - - - +
83H ILE* 4.5 18.8 - - + -
109H ILE* 3.0 44.8 + - + -
135H CYS* 3.9 16.8 - - - -
136H GLU* 1.3 84.1 - - - +
138H TRP* 1.3 67.4 + - - +
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Residues in contact with TRP 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E HIS* 4.8 3.8 - + - -
141E GLN* 5.9 2.2 - - - -
152E ARG* 4.2 8.3 + - - +
44H PHE* 3.8 21.3 - - - -
79H VAL 3.9 0.5 - - - +
80H ILE* 3.8 0.3 - - - -
81H HIS* 3.2 63.4 + + + -
82H HIS* 3.2 57.5 + + + +
103H VAL* 3.9 16.6 - - + -
104H ARG* 3.1 69.6 - - + +
107H LEU* 5.0 0.9 - - + -
108H GLY* 4.0 15.0 - - - +
136H GLU* 4.1 11.0 + - - -
137H VAL* 1.3 80.2 - - - +
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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