Contacts of the strand formed by residues 111 - 115 (chain A) in PDB entry 4RG1
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 GLU 111 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU 3.5 2.4 + - - -
76A SER* 2.7 27.6 + - - +
77A VAL 2.9 25.5 + - - +
109A VAL* 3.3 6.1 - - - +
110A ASP* 1.3 80.9 - - + +
112A ILE* 1.3 66.6 + - - +
113A VAL* 3.7 12.3 - - + -
262A TYR* 4.1 0.2 - - - -
263A THR* 3.2 21.7 + - - +
265A ARG* 2.9 34.7 + - + +
278A PRO* 3.2 22.5 - - - +
279A PHE* 4.1 3.4 - - + -
283A TYR* 2.6 25.9 + - - -
403A 15P 5.4 3.4 - - - -
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Residues in contact with ILE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A VAL 3.3 5.8 - - - +
79A LEU* 3.8 24.0 - - + -
100A ILE* 4.9 2.2 - - + +
101A ALA* 4.7 1.3 - - - -
104A CYS* 3.6 43.1 - - + -
109A VAL* 4.2 1.3 - - + -
111A GLU* 1.3 76.6 - - - +
113A VAL* 1.3 58.4 + - - +
114A VAL* 4.0 1.8 - - + -
146A LEU* 3.7 34.3 - - + -
262A TYR* 3.7 39.3 - - + -
263A THR 2.9 10.3 + - - +
264A VAL* 3.2 7.5 - - + +
265A ARG 2.8 30.5 + - - +
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A VAL 2.8 15.4 + - - +
78A ALA* 3.2 11.1 - - + +
79A LEU* 3.0 28.1 + - - +
111A GLU* 3.7 25.4 - - + +
112A ILE* 1.3 71.4 - - - +
114A VAL* 1.3 62.3 + - - +
115A PHE 3.8 0.3 + - - -
265A ARG* 3.2 49.4 - - + +
267A ALA* 3.9 20.4 - - + -
273A VAL* 4.1 12.1 - - + -
283A TYR* 4.0 2.9 - - - +
308A LEU* 4.7 6.7 - - + -
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU* 3.4 9.0 - - + +
81A GLY* 3.8 26.9 - - - +
112A ILE* 4.5 1.8 - - + -
113A VAL* 1.3 74.6 - - - +
115A PHE* 1.3 60.4 + - - +
139A CYS* 3.8 26.6 - - + +
142A LEU* 3.9 15.7 - - + -
143A ALA* 4.4 10.5 - - + -
146A LEU* 3.9 27.6 - - + -
264A VAL* 4.5 3.4 - - + -
265A ARG 2.8 12.4 + - - +
266A LEU* 3.5 12.8 - - + +
267A ALA 2.9 24.9 + - - +
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Residues in contact with PHE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ALA* 4.2 3.6 - - + -
79A LEU* 3.0 54.6 + - - -
80A PRO* 3.2 16.7 - - + +
81A GLY 3.1 22.3 + - - -
82A SER 4.9 0.2 + - - -
114A VAL* 1.3 74.4 - - - +
116A ASP* 1.3 71.4 + - - +
117A GLU* 3.5 20.9 + - + -
139A CYS* 3.5 4.6 - - - -
267A ALA* 3.2 12.1 - - + +
269A CYS 4.1 3.1 - - - +
270A LEU* 4.1 33.2 - - + -
273A VAL* 3.6 29.8 - - + -
310A VAL* 4.4 7.0 - - + -
311A PHE 3.6 15.3 - - - -
312A GLY* 5.1 0.9 - - - -
317A LEU* 4.2 9.4 - - + -
320A GLY* 4.5 5.8 - - - -
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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