Contacts of the helix formed by residues 90 - 103 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29G TYR* 3.9 25.2 - - + +
86G ARG 3.5 13.2 - - - +
87G TYR* 2.8 23.7 + - - +
89G LEU* 1.3 81.6 - - + +
91G ASN* 1.3 65.4 + - - +
92G ARG* 3.5 8.0 + - - +
93G GLY 3.1 10.9 + - - -
94G ILE* 2.9 22.5 + - - +
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Residues in contact with ASN 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G LEU 3.9 1.0 + - - -
90G THR* 1.3 73.8 - - - +
92G ARG* 1.3 59.7 + - - +
94G ILE* 3.9 8.1 - - - +
95G ALA* 3.1 22.7 + - - +
166G MET* 6.3 0.4 - - - -
170G VAL* 3.9 29.4 - - + +
171G HIS* 5.6 1.2 + - - -
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Residues in contact with ARG 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G ASP* 2.8 29.3 + - - +
87G TYR* 2.8 24.7 - - + +
90G THR* 3.1 7.4 + - - +
91G ASN* 1.3 75.9 - - - +
93G GLY* 1.3 67.6 + - - +
95G ALA* 3.2 25.0 + - - +
96G GLN* 2.9 34.9 + - - +
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Residues in contact with GLY 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G CYS* 4.8 0.2 - - - -
87G TYR* 3.4 38.0 - - - -
88G ILE* 4.0 9.8 - - - +
90G THR* 3.0 10.1 + - - -
92G ARG* 1.3 78.3 - - - +
94G ILE* 1.3 62.5 + - - +
96G GLN* 2.9 15.7 + - - +
97G MET* 2.9 15.6 + - - +
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Residues in contact with ILE 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G ILE 3.2 22.3 + - - +
89G LEU* 3.5 5.2 - - - +
90G THR 2.9 16.6 + - - +
91G ASN* 3.9 6.1 - - - +
93G GLY* 1.3 75.1 - - - +
95G ALA* 1.3 58.0 + - - +
97G MET* 3.8 6.7 - - - +
98G LEU* 2.8 28.8 + - - +
163G PHE* 4.7 4.9 - - + -
166G MET* 3.4 42.2 - - + +
167G LEU* 4.1 17.4 - - + +
170G VAL* 3.7 17.3 - - + -
171G HIS* 3.6 30.7 - - + +
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Residues in contact with ALA 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G ASN 3.1 16.9 + - - +
92G ARG* 3.3 23.1 - - - +
93G GLY 3.1 0.4 - - - -
94G ILE* 1.3 78.2 - - - +
96G GLN* 1.3 61.4 + - - +
98G LEU* 3.4 8.8 + - - +
99G GLU* 3.2 19.6 + - - +
171G HIS* 5.0 7.2 - - + +
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Residues in contact with GLN 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G CYS* 4.1 12.1 - - + +
24G GLU* 3.0 30.1 + - - +
26G ASP* 3.9 2.4 + - - -
87G TYR* 2.4 41.6 + - - -
92G ARG* 2.9 37.2 - - - +
93G GLY 2.9 8.1 + - - +
95G ALA* 1.3 75.4 - - - +
97G MET* 1.3 63.7 - - - +
99G GLU* 3.0 22.4 - - - +
100G LYS* 3.2 13.1 + - + +
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Residues in contact with MET 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G PHE 3.7 10.5 - - - +
23G CYS* 3.9 17.5 - - - -
84G HIS* 4.4 12.3 - - + -
88G ILE* 3.6 21.1 - - + -
93G GLY 2.9 18.1 + - - +
94G ILE 3.9 3.8 - - - +
96G GLN* 1.3 72.2 - - - +
98G LEU* 1.3 61.5 + - - +
99G GLU 3.1 0.2 + - - -
100G LYS* 3.1 23.0 + - - +
101G TYR* 2.8 29.0 + - - +
106G PHE* 3.5 22.8 - - + -
120G LEU* 5.6 0.4 - - + -
121G PRO* 3.7 21.5 - - + -
159G PHE* 4.4 0.2 - - + -
163G PHE* 3.5 35.2 - - + -
167G LEU* 4.7 0.9 - - + -
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Residues in contact with LEU 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G ILE 2.8 18.3 + - - +
95G ALA* 3.5 7.6 - - - +
97G MET* 1.3 76.8 - - - +
99G GLU* 1.3 62.0 + - - +
101G TYR* 3.3 26.5 - - + +
102G GLN* 3.0 30.8 + - - +
167G LEU* 4.1 21.0 - - + +
171G HIS* 3.6 38.1 - - + +
174G TYR* 3.8 37.9 - - + +
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Residues in contact with GLU 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G ALA 3.2 11.8 + - - +
96G GLN* 3.0 14.5 + - - +
97G MET 3.0 0.4 - - - -
98G LEU* 1.3 73.8 - - - +
100G LYS* 1.3 68.4 + - + +
102G GLN* 2.9 30.7 + - - +
103G GLN* 2.7 49.9 + - + +
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Residues in contact with LYS 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G GLU 2.7 24.8 + - - -
21G PHE 4.0 3.0 + - - -
22G PHE 2.9 28.3 - - - -
23G CYS* 3.9 21.8 - - + +
96G GLN 3.4 10.5 - - - +
97G MET* 3.1 20.6 + - - +
99G GLU* 1.3 77.6 - - + +
101G TYR* 1.3 63.9 + - - +
103G GLN* 2.8 15.1 + - - -
105G ASP* 2.9 63.1 + - + +
106G PHE* 3.7 9.2 - - + -
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Residues in contact with TYR 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E LEU* 5.8 4.3 - - + -
97G MET 2.8 13.0 + - - +
98G LEU* 3.3 29.8 - - + +
100G LYS* 1.3 75.2 - - - +
102G GLN* 1.3 64.1 - - - +
104G GLY* 3.0 14.6 + - - -
106G PHE* 3.6 8.7 - - - -
117G GLN* 2.8 23.9 + - - -
118G PRO* 3.3 44.0 - - + +
119G MET 3.6 8.3 - - - -
120G LEU* 3.3 42.6 - - + -
138G PRO* 3.6 8.8 - - - +
167G LEU* 5.3 1.3 - - + -
168G PHE* 4.0 7.7 - + - -
174G TYR* 4.3 30.8 + + + -
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Residues in contact with GLN 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E LEU* 4.4 23.4 - - + +
74E GLN* 4.9 10.6 + - - +
98G LEU* 3.0 24.9 + - + +
99G GLU* 2.9 30.8 + - - +
101G TYR* 1.3 80.0 - - + +
103G GLN* 1.3 67.9 + - - +
104G GLY 3.3 0.6 + - - -
118G PRO* 6.2 0.2 - - - -
174G TYR* 2.6 44.1 + - + -
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Residues in contact with GLN 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E GLN* 6.0 2.0 - - - +
99G GLU* 2.7 43.0 + - + +
100G LYS* 2.8 5.6 + - - +
102G GLN* 1.3 88.5 + - - +
104G GLY* 1.3 62.6 + - - +
105G ASP* 3.1 22.9 + - - +
108G TYR* 3.8 7.1 + - - -
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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