Contacts of the helix formed by residues 101 - 106 (chain B) in PDB entry 3RRA
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 PRO 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B VAL* 1.4 97.7 - - + +
102B VAL* 1.3 65.2 + - - +
103B TYR* 3.4 36.3 - - + +
104B GLU* 3.2 24.4 + - + +
105B LEU* 3.8 1.6 + - - +
298B HIS* 3.8 4.5 - - + -
343B PRO 3.5 19.1 - - - +
344B ARG* 3.8 17.7 - - - +
345B LEU 3.9 6.3 - - - +
346B PRO* 4.5 2.0 - - + -
347B GLY 3.5 9.4 - - - +
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TRP* 3.5 41.5 - - + +
101B PRO* 1.3 71.3 - - - +
103B TYR* 1.3 62.2 + - - +
105B LEU* 3.0 26.5 + - + +
106B LEU* 3.2 26.1 + - + +
265B ILE* 4.4 14.1 - - + -
298B HIS* 3.3 28.8 - - + +
347B GLY* 3.0 27.2 + - - +
348B LEU* 4.1 9.9 - - + +
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Residues in contact with TYR 103 (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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101B PRO* 3.4 17.6 - - + +
102B VAL* 1.3 76.5 - - - +
104B GLU* 1.3 82.5 + - - +
106B LEU* 3.3 6.8 + - - +
107B GLY 3.6 0.5 + - - -
108B GLY* 2.8 23.8 + - - -
109B LEU* 3.7 38.3 - - + +
298B HIS* 3.0 38.8 + + - +
301B PHE* 4.4 9.6 - - + -
302B VAL* 3.6 24.3 - - + +
342B PRO* 3.6 24.9 - - + +
343B PRO* 3.3 33.3 + - + -
344B ARG* 5.4 0.7 - - - -
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Residues in contact with GLU 104 (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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100B VAL* 4.0 27.2 - - + +
101B PRO* 3.2 18.3 + - + +
102B VAL 3.1 0.6 - - - -
103B TYR* 1.3 99.2 + - + +
105B LEU* 1.3 63.9 + - - +
107B GLY* 3.7 7.1 + - - -
108B GLY* 3.7 19.9 + - - +
109B LEU* 4.7 1.0 + - - +
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Residues in contact with LEU 105 (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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91B TRP* 4.0 24.2 - - + -
94B LYS* 3.9 26.5 - - + -
95B GLY* 4.0 20.0 - - - +
98B LEU* 3.8 26.0 - - + -
100B VAL* 3.8 20.2 - - + -
101B PRO 4.0 5.6 - - - +
102B VAL* 3.0 16.3 + - + +
104B GLU* 1.3 77.5 - - - +
106B LEU* 1.3 59.3 + - - +
107B GLY 3.2 5.5 + - - -
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Residues in contact with LEU 106 (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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91B TRP* 3.7 31.9 - - + -
102B VAL* 3.2 25.2 + - + +
103B TYR 3.3 1.3 + - - -
104B GLU 3.3 0.8 - - - -
105B LEU* 1.3 76.0 - - - +
107B GLY* 1.3 58.0 + - - +
108B GLY 3.5 2.0 - - - -
265B ILE* 3.8 26.9 - - + -
269B VAL* 3.9 26.9 - - + -
298B HIS 4.7 5.8 - - - +
302B VAL* 3.7 32.3 - - + +
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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