Contacts of the helix formed by residues 91 - 102 (chain R) in PDB entry 5GAG
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 ASP 91 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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996A A 3.3 44.5 + - - +
997A G 3.6 10.5 - - - +
89R GLU 3.4 1.1 + - - -
90R ILE* 1.3 74.5 - - - +
92R ARG* 1.3 64.6 + - - +
93R LYS* 3.4 5.6 + - - +
94R ILE* 2.9 26.9 + - - +
95R LEU* 2.9 31.3 + - - +
11S GLN* 3.1 40.0 + - - +
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Residues in contact with ARG 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997A G 3.0 30.3 + - - +
998A C 3.3 24.5 + - - -
1153A C 3.0 19.0 + - - -
58R ARG* 3.0 38.4 - - - +
61R TRP* 3.9 21.0 - - + +
62R ILE* 3.8 10.1 - - + -
65R ILE* 3.9 22.4 - - + +
76R TYR* 2.6 23.4 + - - -
80R ILE* 3.9 22.4 - - + +
90R ILE 5.8 0.2 - - - +
91R ASP* 1.3 78.8 - - - +
93R LYS* 1.3 66.3 + - - +
94R ILE 3.2 1.1 - - - -
95R LEU* 5.2 2.9 - - + -
96R ALA* 3.0 26.3 + - - +
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Residues in contact with LYS 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995A C 2.7 55.9 + - - +
996A A 3.0 23.1 + - - +
1K MET 4.7 7.6 + - - +
3K THR* 5.2 3.2 - - + +
61R TRP* 3.5 37.5 + - + +
91R ASP* 3.4 9.4 + - - +
92R ARG* 1.3 76.7 - - - +
94R ILE* 1.3 67.1 + - + +
96R ALA* 4.0 1.9 - - - +
97R ASP* 3.0 29.9 + - + +
11S GLN 3.9 22.2 + - - -
12S HIS* 5.2 5.5 + - - -
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Residues in contact with ILE 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90R ILE* 3.5 22.4 - - + -
91R ASP* 2.9 21.2 + - - +
93R LYS* 1.3 84.9 - - + +
95R LEU* 1.3 58.9 + - - +
97R ASP* 3.3 8.4 - - - +
98R ILE* 2.9 38.1 + - + +
4S VAL* 3.8 28.7 - - + -
11S GLN* 4.0 25.4 - - + +
12S HIS* 4.1 2.2 - - - -
13S ARG* 3.9 33.0 - - + +
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Residues in contact with LEU 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65R ILE* 3.6 27.1 - - + -
79R PHE* 4.1 9.2 - - + -
80R ILE* 4.8 6.7 - - + -
83R LEU* 3.6 25.6 - - + -
90R ILE* 3.7 27.4 - - + +
91R ASP 2.9 23.0 + - - +
92R ARG* 3.4 1.5 + - + -
94R ILE* 1.3 77.4 - - - +
96R ALA* 1.3 58.0 + - - +
98R ILE* 3.1 7.3 + - + +
99R ALA* 2.9 26.7 + - - +
106R PHE* 3.8 10.7 - - + -
109R LEU* 3.6 35.2 - - + -
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Residues in contact with ALA 96 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K THR* 6.1 0.4 - - + -
61R TRP* 3.6 39.0 - - + +
64R ARG* 4.1 17.4 - - + +
65R ILE* 3.9 5.7 - - + +
92R ARG 3.0 16.7 + - - +
93R LYS 4.1 1.6 - - - +
95R LEU* 1.3 76.2 - - - +
97R ASP* 1.3 63.1 + - - +
99R ALA* 3.1 10.7 + - - +
100R VAL* 3.0 27.8 + - - +
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Residues in contact with ASP 97 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K MET* 5.5 7.3 - - - +
3K THR* 6.6 0.2 - - - -
4K PHE* 5.3 4.6 + - - +
64R ARG* 6.3 0.2 - - - +
93R LYS* 3.0 21.5 + - + +
94R ILE* 3.3 12.2 - - + +
96R ALA* 1.3 76.0 - - - +
98R ILE* 1.3 62.9 + - - +
100R VAL* 3.2 4.8 + - - -
101R PHE* 3.0 46.8 + - - +
13S ARG* 2.7 39.7 + - - +
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Residues in contact with ILE 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90R ILE* 5.1 1.6 - - + -
94R ILE* 2.9 38.4 + - + +
95R LEU* 3.4 10.3 - - + +
97R ASP* 1.3 71.8 - - - +
99R ALA* 1.3 57.3 + - - +
102R ASP* 2.7 55.6 + - + +
105R ALA* 4.0 10.5 - - + -
106R PHE* 4.0 24.0 - - + +
109R LEU* 4.4 11.7 - - + -
2S TYR* 4.3 9.2 - - + +
4S VAL* 4.9 3.1 - - + -
13S ARG* 4.5 13.7 - - - +
40S MET* 3.8 28.5 - - - -
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Residues in contact with ALA 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42K ALA* 3.7 12.4 - - + +
64R ARG* 4.8 7.0 - - + +
65R ILE* 5.0 0.9 - - - -
68R ALA* 3.9 20.8 - - + +
95R LEU 2.9 13.9 + - - +
96R ALA* 3.1 14.5 + - - +
98R ILE* 1.3 77.3 - - - +
100R VAL* 1.3 51.9 + - + +
102R ASP 4.5 0.2 - - - -
103R LYS* 2.6 28.0 + - - +
106R PHE* 3.6 28.0 - - + -
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Residues in contact with VAL 100 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K PHE* 3.9 37.9 - - + -
42K ALA 3.5 25.4 - - - +
43K GLU* 4.3 11.5 - - + +
64R ARG* 4.1 21.1 - - - +
96R ALA 3.0 17.4 + - - +
97R ASP* 3.8 5.8 - - - +
99R ALA* 1.3 76.6 - - + +
101R PHE* 1.3 72.3 + - + +
103R LYS* 2.4 30.5 + - - +
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Residues in contact with PHE 101 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K PHE* 4.0 38.4 - + + -
97R ASP* 3.0 34.7 + - - +
100R VAL* 1.3 87.1 - - + +
102R ASP* 1.3 60.0 + - + +
103R LYS* 4.0 4.4 + - - +
13S ARG* 3.8 27.1 - - - +
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Residues in contact with ASP 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98R ILE* 2.7 29.6 + - + +
101R PHE* 1.3 76.3 - - + +
103R LYS* 1.3 63.5 + - - +
104R VAL* 2.9 26.1 + - - +
105R ALA* 3.2 20.4 + - + +
106R PHE* 3.5 14.7 + - - +
2S TYR* 3.1 38.5 + - + +
13S ARG* 5.1 0.7 - - - +
42S ALA* 4.3 4.5 - - - +
45S GLU* 5.8 2.8 + - - -
47S VAL* 5.0 1.2 - - - +
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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