Contacts of the strand formed by residues 111 - 115 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B LEU 3.4 1.6 + - - -
76B SER* 2.7 27.5 + - - +
77B VAL 2.9 26.3 + - - -
109B VAL* 3.2 4.7 + - - +
110B ASP* 1.3 83.6 - - + +
112B ILE* 1.3 67.4 + - - +
113B VAL* 3.7 13.2 - - + +
262B TYR* 4.1 0.2 - - - -
263B THR* 3.2 24.4 - - + +
265B ARG* 2.9 33.1 + - + +
278B PRO* 3.4 21.5 - - + +
279B PHE* 4.3 4.0 - - + -
283B TYR* 2.5 25.9 + - - -
403B 15P 5.4 1.8 - - - -
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Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 3.3 6.3 - - + +
79B LEU* 3.8 22.9 - - + -
100B ILE* 4.7 2.2 - - + +
101B ALA* 4.7 1.8 - - - -
104B CYS* 3.7 39.7 - - + -
109B VAL* 4.3 1.6 - - + -
111B GLU* 1.3 75.3 - - - +
113B VAL* 1.3 63.9 + - - +
114B VAL* 4.4 1.8 - - + -
146B LEU* 3.6 35.9 - - + -
262B TYR* 3.7 39.5 - - + -
263B THR 2.8 11.2 + - - +
264B VAL* 3.3 7.1 - - + +
265B ARG 2.9 24.3 + - - +
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B SER* 5.0 0.4 - - - -
77B VAL 2.7 13.6 + - - +
78B ALA* 3.1 14.1 - - + +
79B LEU* 3.0 28.1 + - - +
111B GLU* 3.7 25.4 - - + +
112B ILE* 1.3 71.6 - - - +
114B VAL* 1.3 62.0 + - - +
115B PHE 3.8 0.3 + - - -
265B ARG* 3.2 48.0 - - + +
267B ALA* 3.9 20.4 - - + -
273B VAL* 4.1 11.9 - - + -
283B TYR* 4.0 2.9 - - - +
308B LEU* 4.8 6.5 - - + -
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 3.3 4.9 - - + -
81B GLY* 3.9 17.3 - - - +
112B ILE* 4.4 5.6 - - + -
113B VAL* 1.3 74.4 - - - +
115B PHE* 1.3 59.9 + - - +
139B CYS* 3.8 37.3 - - + +
142B LEU* 4.0 15.5 - - + -
143B ALA* 4.6 3.6 - - + -
146B LEU* 3.9 27.6 - - + -
264B VAL* 4.5 11.7 - - + -
265B ARG 2.8 10.0 + - - +
266B LEU* 3.4 12.9 - - + +
267B ALA 2.9 24.2 + - - +
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Residues in contact with PHE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ALA* 4.2 4.7 - - + -
79B LEU* 3.0 50.0 + - - -
80B PRO* 3.2 32.4 - - + +
81B GLY 3.2 7.6 + - - -
113B VAL 5.1 0.2 - - - +
114B VAL* 1.3 75.2 - - - +
116B ASP* 1.3 70.1 + - - +
117B GLU* 3.5 22.6 + - + -
139B CYS* 3.6 4.6 - - - -
267B ALA* 3.2 12.3 - - + +
269B CYS 4.0 3.6 - - - +
270B LEU* 4.1 33.0 - - + -
273B VAL* 3.6 30.5 - - + -
310B VAL* 4.4 8.1 - - + -
311B PHE 3.6 15.7 - - - -
312B GLY* 5.0 1.1 - - - -
317B LEU* 4.2 9.2 - - + -
320B GLY* 4.6 4.9 - - - -
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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