Contacts of the helix formed by residues 90 - 103 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29J TYR* 4.0 26.1 - - + +
86J ARG 3.7 11.2 - - - +
87J TYR* 2.8 24.4 + - - +
89J LEU* 1.3 81.4 - - + +
91J ASN* 1.3 66.0 + - - +
92J ARG* 3.5 7.6 + - - +
93J GLY 3.1 10.6 + - - -
94J ILE* 2.9 23.7 + - - +
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Residues in contact with ASN 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89J LEU 4.0 1.2 + - - -
90J THR* 1.3 73.4 - - - +
92J ARG* 1.3 57.6 + - - +
94J ILE* 3.9 7.6 - - - +
95J ALA* 3.1 26.3 + - - +
166J MET* 5.8 1.2 - - - +
170J VAL* 3.9 28.8 - - + +
171J HIS* 5.6 1.2 + - - -
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Residues in contact with ARG 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J ASP* 2.9 28.8 + - - +
87J TYR* 2.8 25.6 - - + +
90J THR* 3.1 7.2 + - - +
91J ASN* 1.3 75.4 - - - +
93J GLY* 1.3 67.2 + - - +
95J ALA* 3.1 17.7 + - - +
96J GLN* 2.9 42.5 + - - +
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Residues in contact with GLY 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J CYS* 4.7 0.4 - - - -
87J TYR* 3.4 39.1 - - - -
88J ILE* 4.0 9.9 - - - -
90J THR* 3.0 10.5 + - - -
92J ARG* 1.3 76.1 - - - +
94J ILE* 1.3 63.2 + - - +
96J GLN* 2.9 14.8 + - - +
97J MET* 2.9 16.9 + - - +
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Residues in contact with ILE 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88J ILE 3.2 21.9 + - - +
89J LEU 3.5 5.4 - - - +
90J THR 2.9 16.8 + - - +
91J ASN* 3.9 7.0 - - - +
93J GLY* 1.3 75.0 - - - +
95J ALA* 1.3 58.6 + - - +
97J MET* 3.8 5.9 - - - +
98J LEU* 2.8 28.2 + - - +
163J PHE* 4.7 4.5 - - + -
166J MET* 3.4 42.6 - - + +
167J LEU* 4.1 17.9 - - + +
170J VAL* 3.8 16.6 - - + -
171J HIS* 3.7 29.6 - - + +
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Residues in contact with ALA 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J ASN 3.1 16.5 + - - +
92J ARG* 3.3 22.0 - - - +
93J GLY 3.1 0.4 - - - -
94J ILE* 1.3 77.7 - - - +
96J GLN* 1.3 62.5 + - - +
98J LEU* 3.3 8.1 + - - +
99J GLU* 3.1 19.8 + - - +
171J HIS* 5.0 7.0 - - + +
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Residues in contact with GLN 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J CYS* 4.0 11.8 - - + +
24J GLU* 3.0 32.4 + - - +
26J ASP* 4.0 2.2 + - - -
87J TYR* 2.4 42.3 + - - -
92J ARG* 2.9 37.4 + - - +
93J GLY 2.9 7.4 + - - +
95J ALA* 1.3 74.4 - - - +
97J MET* 1.3 64.9 + - - +
99J GLU* 3.1 22.6 - - - +
100J LYS* 3.2 13.3 + - - +
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Residues in contact with MET 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J PHE 3.5 18.8 - - - +
23J CYS* 3.9 24.0 - - - -
84J HIS* 4.4 2.7 - - + -
88J ILE* 3.6 28.9 - - + -
93J GLY 2.9 18.1 + - - +
94J ILE 3.9 2.9 - - - +
96J GLN* 1.3 73.6 - - - +
98J LEU* 1.3 55.0 + - - +
100J LYS* 3.1 11.5 + - - +
101J TYR* 2.8 35.4 + - - +
106J PHE* 3.5 23.9 - - + -
121J PRO* 3.7 19.7 - - + -
159J PHE* 4.4 3.1 - - + -
163J PHE* 3.5 34.5 - - + -
167J LEU* 4.7 1.3 - - + -
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Residues in contact with LEU 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94J ILE 2.8 18.5 + - - +
95J ALA* 3.4 7.6 - - - +
97J MET* 1.3 77.5 - - - +
99J GLU* 1.3 62.5 + - - +
101J TYR* 3.3 26.9 - - + +
102J GLN* 3.0 28.8 + - - +
167J LEU* 4.0 20.8 - - + +
171J HIS* 3.7 38.4 - - + +
174J TYR* 3.9 36.6 - - + +
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Residues in contact with GLU 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95J ALA 3.1 11.5 + - - +
96J GLN* 3.1 15.4 + - - +
97J MET 3.0 0.2 - - - -
98J LEU* 1.3 76.9 - - - +
100J LYS* 1.3 65.2 + - + +
102J GLN* 2.9 31.4 + - - +
103J GLN* 2.6 48.7 + - + +
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Residues in contact with LYS 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J GLU 2.5 26.0 + - - -
21J PHE 4.0 3.0 - - - -
22J PHE 2.8 29.2 - - - +
23J CYS* 3.9 21.5 - - + +
96J GLN 3.4 9.9 - - - +
97J MET* 3.1 19.2 + - - +
99J GLU* 1.3 77.2 - - + +
101J TYR* 1.3 63.4 + - - +
103J GLN* 2.9 14.2 + - - -
105J ASP* 2.9 63.4 + - + +
106J PHE* 3.7 8.2 - - + -
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Residues in contact with TYR 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97J MET 2.8 17.0 + - - +
98J LEU* 3.3 29.2 - - + +
100J LYS* 1.3 73.1 - - - +
102J GLN* 1.3 64.6 + - + +
104J GLY* 3.0 14.6 + - - -
105J ASP 5.0 0.2 - - - +
106J PHE* 3.6 8.4 - - - -
117J GLN* 2.8 23.2 + - - -
118J PRO* 3.3 44.1 - - + +
119J MET 3.7 8.1 - - - -
120J LEU* 3.4 42.8 - - + -
138J PRO* 3.6 9.5 - - - +
167J LEU* 5.3 1.6 - - + -
168J PHE* 4.0 8.3 - + - -
174J TYR* 4.3 31.2 + + + -
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Residues in contact with GLN 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98J LEU* 3.0 24.7 + - + +
99J GLU* 2.9 32.5 + - - +
101J TYR* 1.3 78.6 - - + +
103J GLN* 1.3 68.4 + - - +
104J GLY 3.3 0.7 + - - -
118J PRO* 6.2 0.2 - - - -
174J TYR* 2.7 44.1 + - + -
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Residues in contact with GLN 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99J GLU* 2.6 42.3 + - + +
100J LYS* 2.9 5.6 + - - +
102J GLN* 1.3 87.4 + - - +
104J GLY* 1.3 63.1 + - - +
105J ASP* 3.1 22.5 + - - +
108J TYR* 3.8 7.3 + - - -
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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