Contacts of the strand formed by residues 74 - 80 (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 THR 74 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B PRO 5.5 0.4 - - - +
73B TYR* 1.3 85.4 - - - +
75B LEU* 1.3 61.4 + - - +
76B SER* 4.8 2.2 + - - -
110B ASP* 3.2 16.6 - - + +
250B GLN* 5.1 1.3 - - - +
253B ARG* 3.4 33.7 - - - +
279B PHE* 3.4 25.9 - - + -
304B PHE* 3.8 0.3 - - - -
305B ARG 2.9 7.3 + - - -
306B HIS* 2.8 37.9 + - + +
307B ALA* 2.9 25.1 + - - +
403B 15P 5.7 1.3 - - - -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TYR* 4.7 12.8 - - + -
74B THR* 1.3 73.6 - - - +
76B SER* 1.3 68.1 + - - +
77B VAL* 5.0 0.4 - - + -
107B PHE* 3.8 24.0 - - + +
108B CYS 4.4 6.3 - - - +
109B VAL* 3.6 20.0 - - + +
110B ASP* 2.8 40.7 + - - +
111B GLU 3.4 2.8 + - - -
307B ALA* 3.6 12.3 - - + +
309B VAL* 4.0 26.9 - - + -
361B LEU* 4.5 11.9 - - + -
368B LEU* 4.0 25.1 - - + -
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Residues in contact with SER 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B THR* 4.8 1.2 + - - -
75B LEU* 1.3 78.7 + - - +
77B VAL* 1.3 65.3 + - - +
110B ASP* 5.4 0.2 - - - +
111B GLU* 2.7 42.9 + - - +
113B VAL* 5.0 0.4 - - - -
279B PHE* 4.2 7.1 - - - -
283B TYR* 3.4 17.3 - - - -
307B ALA 2.8 14.0 + - - +
308B LEU* 3.4 9.9 - - - -
309B VAL 2.9 25.6 + - - -
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 5.0 1.1 - - + -
76B SER* 1.3 79.2 - - - +
78B ALA* 1.3 60.6 + - - +
79B LEU* 4.8 6.1 - - + -
104B CYS* 4.1 22.0 - - - -
109B VAL* 3.7 28.5 - - + -
111B GLU 2.9 7.0 + - - +
112B ILE* 3.3 5.2 - - + +
113B VAL* 2.7 32.1 + - - +
308B LEU* 4.5 2.7 - - - -
309B VAL* 3.3 7.0 - - + +
311B PHE* 3.9 23.1 - - + -
357B ILE* 4.5 10.1 - - + -
361B LEU* 4.0 24.0 - - + -
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Residues in contact with ALA 78 (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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77B VAL* 1.3 76.0 - - - +
79B LEU* 1.3 60.3 + - - +
113B VAL* 3.1 14.8 - - + +
115B PHE* 4.2 6.5 - - + -
273B VAL* 3.7 30.5 - - + -
308B LEU* 4.2 6.7 - - + +
309B VAL 2.9 7.7 + - - -
310B VAL* 4.2 13.5 - - + -
311B PHE* 2.8 34.2 + - - -
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Residues in contact with LEU 79 (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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77B VAL* 4.8 4.3 - - + -
78B ALA* 1.3 78.0 - - - +
80B PRO* 1.3 74.8 - - + +
83B ILE* 3.8 17.5 - - + -
100B ILE* 3.6 42.8 - - + -
112B ILE* 3.8 23.3 - - + -
113B VAL 3.0 16.5 + - - +
114B VAL* 3.3 11.9 - - + -
115B PHE* 3.0 26.7 + - - -
142B LEU* 4.4 7.0 - - + -
311B PHE* 3.6 14.6 - - + +
353B THR* 4.2 2.9 - - + -
357B ILE* 4.1 9.9 - - + -
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Residues in contact with PRO 80 (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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79B LEU* 1.3 94.6 - - + +
81B GLY* 1.3 64.1 + - - +
82B SER* 3.2 13.5 + - - +
83B ILE* 3.5 20.3 + - + +
114B VAL* 4.7 0.2 - - - -
115B PHE* 3.2 21.5 - - + +
117B GLU* 3.8 23.3 - - + +
142B LEU* 4.4 0.2 - - - +
311B PHE 3.4 14.1 - - - +
312B GLY 3.7 7.4 - - - +
313B GLY* 3.4 29.2 - - - +
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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