Contacts of the helix formed by residues 91 - 101 (chain B) in PDB entry 1RPU
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 91 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LYS* 4.0 25.8 + - - +
88B GLY* 4.6 6.1 - - - +
90B TRP* 1.3 88.0 - - - +
92B GLY* 1.3 66.6 + - - +
93B ASP* 3.5 11.3 + - - +
94B SER* 2.8 28.8 + - - -
95B VAL* 3.0 25.1 + - - +
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Residues in contact with GLY 92 (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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90B TRP* 4.6 1.8 - - - -
91B THR* 1.3 73.6 - - - +
93B ASP* 1.3 57.4 + - - +
95B VAL* 3.8 1.4 - - - +
96B ASN* 3.0 42.4 + - - -
131B GLN* 5.5 4.3 - - - -
134B CYS* 4.6 18.4 - - - -
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Residues in contact with ASP 93 (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 THR* 3.1 10.2 + - - +
92B GLY* 1.3 73.1 - - - +
94B SER* 1.3 66.4 + - - +
96B ASN* 3.3 3.9 + - - +
97B TYR* 2.9 29.3 + - - +
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Residues in contact with SER 94 (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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28B SER 4.1 3.2 - - - +
29B PRO* 2.7 27.4 + - - +
31B LYS* 3.6 24.2 - - - -
90B TRP* 3.6 1.6 - - - +
91B THR* 2.8 34.6 + - - -
93B ASP* 1.3 77.3 - - - +
95B VAL* 1.3 57.2 + - - +
97B TYR* 4.2 4.3 - - - +
98B ALA* 3.1 31.4 + - - +
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Residues in contact with VAL 95 (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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29B PRO* 4.2 9.0 - - + +
63B TRP* 3.7 29.6 - - + +
65B PHE* 3.8 20.5 - - + -
90B TRP* 3.4 28.0 - - + -
91B THR 3.0 21.3 + - - +
92B GLY 3.8 2.9 - - - +
94B SER* 1.3 80.2 + - - +
96B ASN* 1.3 61.8 + - - +
98B ALA* 3.5 2.3 + - - +
99B ALA* 2.8 27.9 + - - +
130B LEU* 4.2 6.5 - - + -
134B CYS* 3.7 20.6 - - - -
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Residues in contact with ASN 96 (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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92B GLY* 3.0 28.6 + - - +
93B ASP* 4.0 3.8 - - - +
95B VAL* 1.3 72.6 - - - +
97B TYR* 1.3 70.3 + - - +
99B ALA* 3.0 6.5 + - - +
100B SER* 2.9 20.1 + - - -
130B LEU* 3.1 26.9 - - - +
131B GLN* 3.1 27.2 + - - +
134B CYS* 4.9 5.2 - - - -
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Residues in contact with TYR 97 (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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27B THR* 3.9 21.3 + - + +
93B ASP 2.9 18.3 + - - +
94B SER* 4.2 3.4 - - - +
96B ASN* 1.3 76.9 - - - +
98B ALA* 1.3 66.1 + - + +
99B ALA 2.8 1.0 + - - -
100B SER* 2.3 37.3 + - - -
101B ARG* 3.6 20.0 + - + +
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Residues in contact with ALA 98 (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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27B THR* 3.7 17.3 - - + +
28B SER* 3.4 10.1 - - - +
29B PRO* 3.4 34.5 - - + -
65B PHE* 4.4 2.0 - - + -
94B SER 3.1 19.1 + - - +
95B VAL 3.8 2.2 - - - +
97B TYR* 1.3 80.2 - - + +
99B ALA* 1.3 57.5 + - - +
101B ARG* 3.7 3.5 + - - +
102B PHE* 2.8 31.4 - - + -
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Residues in contact with ALA 99 (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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65B PHE* 3.7 27.8 - - + +
95B VAL 2.8 18.6 + - - +
96B ASN 3.3 5.4 - - - +
97B TYR 2.8 1.2 + - - -
98B ALA* 1.3 77.3 - - - +
100B SER* 1.3 53.1 + - - +
102B PHE* 2.8 13.8 + - - +
103B LEU* 2.8 32.0 + - - -
110B CYS* 6.0 0.4 - - - -
130B LEU* 3.8 19.5 - - + -
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Residues in contact with SER 100 (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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96B ASN 2.9 10.5 + - - -
97B TYR* 2.3 45.1 + - - -
99B ALA* 1.3 76.7 - - - +
101B ARG* 1.3 56.4 + - - +
102B PHE 2.8 7.1 + - - -
103B LEU* 2.9 41.5 - - - +
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Residues in contact with ARG 101 (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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27B THR* 3.5 35.9 - - + +
97B TYR* 3.6 22.1 + - + +
98B ALA 4.0 8.5 - - - +
99B ALA 3.1 1.6 - - - -
100B SER* 1.3 75.2 + - - +
102B PHE* 1.3 76.6 + - + +
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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