Contacts of the helix formed by residues 90 - 103 (chain B) in PDB entry 1RQF
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 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B TYR* 3.7 29.9 - - + +
86B ARG 3.7 9.9 - - - +
87B TYR* 2.7 23.6 + - - +
89B LEU* 1.3 80.8 - - + +
91B ASN* 1.3 65.1 + - - +
92B ARG* 3.5 7.5 + - - +
93B GLY 3.1 10.6 + - - -
94B ILE* 2.9 24.7 + - - +
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Residues in contact with ASN 91 (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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89B LEU 4.0 1.0 + - - -
90B THR* 1.3 74.1 - - - +
92B ARG* 1.3 60.8 + - - +
94B ILE* 4.0 7.2 - - - +
95B ALA* 3.1 22.2 + - - +
166B MET* 5.7 0.6 - - - +
170B VAL* 3.9 29.3 - - + +
171B HIS* 5.6 1.4 + - - -
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Residues in contact with ARG 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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26B ASP* 2.7 28.7 + - - +
87B TYR* 2.8 24.7 - - + +
90B THR* 3.1 8.1 + - - +
91B ASN* 1.3 77.2 - - - +
93B GLY* 1.3 64.7 + - - +
95B ALA* 3.1 18.3 + - - +
96B GLN* 2.9 41.9 + - - +
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Residues in contact with GLY 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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23B CYS* 4.7 0.4 - - - -
87B TYR* 3.4 38.3 - - - -
88B ILE* 4.0 9.6 - - - -
90B THR* 3.1 10.5 + - - -
92B ARG* 1.3 76.6 - - - +
94B ILE* 1.3 62.7 + - - +
96B GLN* 3.0 6.6 + - - +
97B MET* 2.9 25.0 + - - +
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Residues in contact with ILE 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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88B ILE 3.2 21.6 + - - +
89B LEU* 3.5 5.8 - - - +
90B THR 2.9 17.7 + - - +
91B ASN* 4.0 6.3 - - - +
93B GLY* 1.3 74.1 - - - +
95B ALA* 1.3 58.7 + - - +
97B MET* 3.3 6.2 + - - +
98B LEU* 2.8 28.4 + - - +
163B PHE* 4.8 4.5 - - + -
166B MET* 3.4 42.6 - - + +
167B LEU* 4.1 17.9 - - + -
170B VAL* 3.8 16.6 - - + -
171B HIS* 3.7 30.5 - - + +
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Residues in contact with ALA 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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91B ASN 3.1 16.7 + - - +
92B ARG* 3.2 22.7 - - - +
93B GLY 3.1 0.2 - - - -
94B ILE* 1.3 78.4 - - - +
96B GLN* 1.3 62.1 + - - +
98B LEU* 3.3 9.2 + - - +
99B GLU* 3.1 19.8 + - - +
171B HIS* 5.0 7.2 + - + +
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Residues in contact with GLN 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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23B CYS* 4.2 11.2 - - + +
24B GLU* 3.0 34.9 + - - +
26B ASP* 3.7 2.6 + - - -
87B TYR* 2.4 38.2 + - - -
92B ARG* 2.9 35.8 - - - +
93B GLY 3.0 8.3 + - - +
95B ALA* 1.3 77.2 - - - +
97B MET* 1.3 61.8 + - - +
99B GLU* 3.0 22.5 - - - +
100B LYS* 3.2 13.1 + - - +
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Residues in contact with MET 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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21B PHE 3.6 13.7 - - - +
23B CYS* 3.8 26.2 - - - -
84B HIS* 4.4 1.3 - - + -
88B ILE* 3.6 28.0 - - + -
93B GLY 2.9 18.3 + - - +
94B ILE 3.8 3.1 - - - +
96B GLN* 1.3 72.4 - - - +
98B LEU* 1.3 61.7 + - - +
100B LYS* 3.1 15.3 + - - +
101B TYR* 2.8 28.8 + - - +
106B PHE* 3.5 25.5 - - + -
121B PRO* 3.7 18.4 - - + -
159B PHE* 4.4 2.7 - - + -
163B PHE* 3.5 35.7 - - + -
167B LEU* 4.6 1.6 - - + -
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Residues in contact with LEU 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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94B ILE 2.8 18.6 + - - +
95B ALA* 3.4 7.2 - - - +
96B GLN 3.2 0.2 - - - -
97B MET* 1.3 76.0 - - - +
99B GLU* 1.3 62.8 + - - +
101B TYR* 3.3 26.5 - - + +
102B GLN* 3.0 28.8 + - - +
167B LEU* 4.1 20.6 - - + +
171B HIS* 3.7 37.7 - - + +
174B TYR* 3.8 38.1 - - + +
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Residues in contact with GLU 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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95B ALA 3.1 11.3 + - - +
96B GLN* 3.0 15.4 + - - +
98B LEU* 1.3 76.6 - - - +
100B LYS* 1.3 66.3 + - + +
102B GLN* 2.9 31.3 + - - +
103B GLN* 2.6 47.8 + - + +
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Residues in contact with LYS 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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20B GLU 2.8 23.6 + - - -
21B PHE 4.3 1.1 - - - -
22B PHE 3.0 26.9 - - - -
23B CYS* 4.0 11.7 - - + +
96B GLN 3.4 11.2 - - - +
97B MET* 3.1 28.9 + - - +
99B GLU* 1.3 76.1 - - + +
101B TYR* 1.3 63.4 + - - +
103B GLN* 2.9 14.5 + - - -
105B ASP* 2.9 64.9 + - + +
106B PHE* 3.7 10.7 - - + -
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Residues in contact with TYR 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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97B MET 2.8 13.4 + - - +
98B LEU* 3.3 29.2 - - + +
100B LYS* 1.3 76.0 - - - +
102B GLN* 1.3 63.4 + - + +
104B GLY* 3.0 14.9 + - - -
105B ASP 5.0 0.2 - - - +
106B PHE* 3.6 8.9 - - - -
117B GLN* 2.9 23.0 + - - -
118B PRO* 3.3 43.3 - - + +
119B MET 3.7 8.3 - - - -
120B LEU* 3.4 42.0 - - + -
138B PRO* 3.6 9.5 - - - +
167B LEU* 5.4 1.3 - - + -
168B PHE* 3.9 8.7 - + - -
174B TYR* 4.3 31.5 + + + -
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Residues in contact with GLN 102 (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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98B LEU* 3.0 24.0 + - + +
99B GLU* 2.9 32.5 + - - +
101B TYR* 1.3 80.2 - - + +
103B GLN* 1.3 67.2 + - - +
104B GLY 3.3 1.1 + - - -
118B PRO* 6.1 0.4 - - - -
174B TYR* 2.6 45.1 + - + -
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Residues in contact with GLN 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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99B GLU* 2.6 40.5 + - + +
100B LYS* 2.9 6.5 + - - +
102B GLN* 1.3 87.8 + - - +
104B GLY* 1.3 62.9 + - - +
105B ASP* 3.1 22.2 + - - +
108B TYR* 3.7 8.0 + - - -
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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