Contacts of the helix formed by residues 90 - 103 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29H TYR* 3.5 35.6 - - + +
86H ARG 3.8 4.9 - - - +
87H TYR* 2.8 24.0 + - - +
89H LEU* 1.3 80.8 - - + +
91H ASN* 1.3 65.9 + - - +
92H ARG* 3.4 7.1 + - - +
93H GLY 3.1 10.6 + - - -
94H ILE* 2.9 22.3 + - - +
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Residues in contact with ASN 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89H LEU 3.9 1.2 + - - -
90H THR* 1.3 72.4 - - - +
92H ARG* 1.3 56.1 + - - +
94H ILE* 3.9 8.1 - - - +
95H ALA* 3.1 25.8 + - - +
166H MET* 5.8 0.4 - - - +
170H VAL* 3.9 29.3 - - + +
171H HIS* 5.6 1.4 + - - -
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Residues in contact with ARG 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H ASP* 2.5 30.4 + - - +
29H TYR* 6.4 0.2 - - + -
87H TYR* 2.8 24.7 - - + +
90H THR* 3.1 7.4 + - - +
91H ASN* 1.3 76.1 - - - +
93H GLY* 1.3 67.0 - - - +
95H ALA* 3.2 24.5 + - - +
96H GLN* 2.9 35.0 + - - +
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Residues in contact with GLY 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H CYS* 4.8 0.4 - - - -
87H TYR* 3.4 38.3 - - - -
88H ILE* 4.0 9.4 - - - -
90H THR* 3.0 10.3 + - - -
92H ARG* 1.3 77.1 - - - +
94H ILE* 1.3 61.9 + - - +
96H GLN* 2.9 15.4 + - - +
97H MET* 2.9 15.9 + - - +
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Residues in contact with ILE 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88H ILE 3.2 22.3 + - - +
89H LEU* 3.5 6.1 - - - +
90H THR 2.9 16.8 + - - +
91H ASN* 3.9 7.0 - - - +
93H GLY* 1.3 74.1 - - - +
95H ALA* 1.3 57.6 + - - +
97H MET* 3.9 6.1 - - - +
98H LEU* 2.8 28.6 + - - +
163H PHE* 4.8 4.3 - - + -
166H MET* 3.4 42.0 - - + +
167H LEU* 4.1 18.6 - - + +
170H VAL* 3.8 17.0 - - + -
171H HIS* 3.6 30.5 - - + +
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Residues in contact with ALA 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H ASN 3.1 15.7 + - - +
92H ARG* 3.3 22.9 - - - +
93H GLY 3.1 0.4 - - - -
94H ILE* 1.3 80.0 - - - +
96H GLN* 1.3 61.2 + - - +
98H LEU* 3.4 9.1 + - - +
99H GLU* 3.2 19.2 + - - +
171H HIS* 5.0 7.4 + - + +
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Residues in contact with GLN 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H CYS* 4.2 11.5 - - + +
24H GLU* 2.9 34.3 + - - +
26H ASP* 3.6 2.8 + - - -
87H TYR* 2.4 39.0 + - - -
92H ARG* 2.9 36.8 + - - +
93H GLY 2.9 8.3 + - - +
95H ALA* 1.3 74.5 - - - +
97H MET* 1.3 65.5 + - - +
99H GLU* 3.0 22.8 - - - +
100H LYS* 3.2 13.4 + - - +
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Residues in contact with MET 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H PHE 3.7 11.0 - - - +
23H CYS* 3.8 27.6 - - - -
84H HIS* 4.4 5.6 - - + -
88H ILE* 3.6 32.1 - - + -
93H GLY 2.9 12.8 + - - +
94H ILE 3.9 2.7 - - - +
96H GLN* 1.3 71.9 - - - +
98H LEU* 1.3 55.7 + - - +
100H LYS* 3.1 14.0 + - - +
101H TYR* 2.7 36.0 + - - +
106H PHE* 3.6 23.2 - - + -
120H LEU* 5.7 0.2 - - + -
121H PRO* 3.7 21.1 - - + -
163H PHE* 3.5 35.4 - - + -
167H LEU* 4.6 1.8 - - + -
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Residues in contact with LEU 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94H ILE 2.8 18.0 + - - +
95H ALA* 3.5 7.9 - - - +
97H MET* 1.3 76.2 - - - +
99H GLU* 1.3 61.9 + - - +
101H TYR* 3.3 26.4 - - + +
102H GLN* 3.0 29.1 + - - +
167H LEU* 4.1 20.3 - - + +
171H HIS* 3.6 37.5 - - + +
174H TYR* 3.9 37.7 - - + +
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Residues in contact with GLU 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H ALA 3.2 11.5 + - - +
96H GLN* 3.0 15.0 + - - +
97H MET 3.0 0.4 - - - -
98H LEU* 1.3 74.2 - - - +
100H LYS* 1.3 67.9 + - + +
102H GLN* 2.9 30.9 + - - +
103H GLN* 2.7 49.1 + - + +
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Residues in contact with LYS 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H GLU 2.8 23.4 + - - -
21H PHE 4.2 1.1 - - - -
22H PHE 2.9 27.4 - - - -
23H CYS* 3.8 22.7 - - + +
96H GLN 3.4 9.4 - - - +
97H MET* 3.1 19.2 + - - +
99H GLU* 1.3 77.0 - - + +
101H TYR* 1.3 63.3 + - - +
103H GLN* 2.8 14.9 + - - -
105H ASP* 2.9 65.2 + - + +
106H PHE* 3.7 11.3 - - + -
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Residues in contact with TYR 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H MET 2.7 17.0 + - - +
98H LEU* 3.3 29.4 - - + +
100H LYS* 1.3 71.9 - - - +
102H GLN* 1.3 64.4 + - + +
104H GLY* 3.0 14.4 + - - -
105H ASP 5.0 0.2 - - - +
106H PHE* 3.6 9.7 - - - -
117H GLN* 2.8 24.4 + - - -
118H PRO* 3.3 43.6 - - + +
119H MET 3.7 7.9 - - - -
120H LEU* 3.3 42.8 - - + -
138H PRO* 3.6 9.0 - - - +
167H LEU* 5.3 1.3 - - + -
168H PHE* 4.0 9.1 - + - -
174H TYR* 4.3 31.4 + + + -
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Residues in contact with GLN 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H LEU* 3.0 26.7 + - + +
99H GLU* 2.9 31.3 + - - +
101H TYR* 1.3 79.2 - - + +
103H GLN* 1.3 68.9 + - - +
104H GLY 3.6 0.2 + - - -
118H PRO* 6.1 0.4 - - - -
174H TYR* 2.7 44.3 + - + -
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Residues in contact with GLN 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H GLU* 2.7 43.6 + - + +
100H LYS* 2.8 5.8 + - - +
102H GLN* 1.3 88.0 + - - +
104H GLY* 1.3 63.6 + - - +
105H ASP* 3.1 22.1 + - - +
108H 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