Contacts of the helix formed by residues 80 - 97 (chain R) in PDB entry 2DYS
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 GLU 80 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78R HIS* 3.0 11.5 + - + +
79R LYS* 1.3 86.6 + - - +
81R ILE* 1.3 66.3 + - + +
83R PRO* 3.5 12.7 - - + +
84R TYR* 3.7 14.7 + - - +
4V LEU* 5.8 0.3 - - - +
5V ALA 5.5 0.3 - - - +
7V PRO* 4.0 19.9 - - + +
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Residues in contact with ILE 81 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R VAL* 3.9 26.0 - - + -
75R ALA* 3.9 7.2 - - + -
78R HIS* 3.1 26.6 + - + +
80R GLU* 1.3 78.2 - - + +
82R TYR* 1.3 66.3 + - - +
84R TYR* 3.2 4.7 + - - +
85R VAL* 3.0 26.9 + - + +
7V PRO* 3.6 18.6 - - + -
8V GLN 3.1 26.7 - - - +
9V MET* 3.8 23.6 - - + -
12V LEU* 3.8 22.2 - - + -
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Residues in contact with TYR 82 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68R LEU* 3.6 22.2 - - + +
71R VAL* 4.7 9.8 + - + -
72R LYS* 3.7 52.9 - - + +
75R ALA* 4.8 3.9 - - + +
78R HIS 4.6 1.4 + - - -
79R LYS 4.4 1.5 + - - +
81R ILE* 1.3 74.0 - - - +
83R PRO* 1.4 68.6 - - + +
85R VAL* 2.8 8.5 + - + +
86R ILE* 2.8 65.9 + - + +
100R THR* 4.0 0.5 - - - -
101R PRO* 3.3 21.2 - - + +
102R GLU* 2.7 41.5 + - - -
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Residues in contact with PRO 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79R LYS 3.0 26.9 - - - +
80R GLU* 3.5 9.2 - - - +
81R ILE 3.4 4.5 - - - -
82R TYR* 1.4 99.8 - - + +
84R TYR* 1.3 56.5 + - - +
86R ILE* 3.6 7.5 + - + +
87R GLN* 3.0 26.5 + - - +
4V LEU* 3.5 19.4 - - + +
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Residues in contact with TYR 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R PRO* 4.0 17.0 - - + +
80R GLU 3.7 10.9 + - - +
81R ILE 3.2 7.1 + - - +
82R TYR 3.2 0.8 - - - -
83R PRO* 1.3 79.2 - - - +
85R VAL* 1.3 73.6 + - + +
87R GLN* 3.1 13.6 - - - +
88R GLU* 3.0 60.0 + - + +
4V LEU* 3.7 29.6 - - + +
5V ALA 3.7 2.7 - - - +
6V LYS* 3.4 50.7 - - + +
7V PRO* 3.6 20.6 - - + -
9V MET* 4.3 8.5 - - - -
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Residues in contact with VAL 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43R PRO 5.0 0.4 - - - +
45R PRO* 4.4 14.4 - - + -
48R ILE* 4.7 5.8 - - + -
68R LEU* 5.8 0.9 - - + -
71R VAL* 4.2 24.0 - - + -
81R ILE* 3.0 19.0 + - + +
82R TYR* 2.8 8.5 + - + +
84R TYR* 1.3 82.9 - - + +
86R ILE* 1.3 69.1 + - + +
88R GLU* 3.0 6.4 + - - +
89R LEU* 2.9 48.3 + - + +
9V MET* 3.7 30.1 - - + -
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Residues in contact with ILE 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68R LEU* 3.9 23.1 - - + -
82R TYR* 2.8 60.6 + - + +
83R PRO* 3.9 7.2 - - + +
85R VAL* 1.3 76.5 - - + +
87R GLN* 1.3 65.1 + - - +
89R LEU* 3.1 5.5 + - + +
90R ARG* 3.0 46.1 + - - +
93R LEU* 4.0 14.8 - - + +
100R THR* 4.1 10.5 - - + -
102R GLU* 5.2 0.2 - - - +
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Residues in contact with GLN 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R PRO 3.0 16.6 + - - +
84R TYR* 3.1 16.9 - - - +
86R ILE* 1.3 79.5 - - - +
88R GLU* 1.3 84.8 + - - +
89R LEU 3.2 0.9 + - - -
90R ARG* 3.3 20.8 + - - +
91R PRO* 4.2 2.3 - - - +
3V ALA* 3.5 14.9 - - - +
4V LEU* 2.7 54.4 + - + +
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Residues in contact with GLU 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R PRO* 3.8 22.0 - - + +
84R TYR* 3.0 46.6 + - + +
85R VAL 3.0 6.9 + - - +
87R GLN* 1.3 104.4 + - - +
89R LEU* 1.3 62.9 + - - +
90R ARG 3.4 0.2 - - - -
91R PRO* 3.8 9.7 - - - +
92R THR* 5.5 0.9 + - - -
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Residues in contact with LEU 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R PRO* 3.4 32.8 - - + +
48R ILE* 3.6 27.1 - - + -
49R ASP* 4.1 19.1 - - + +
52R LEU* 4.3 6.1 - - + -
68R LEU* 4.0 15.3 - - + -
85R VAL* 2.9 35.1 + - + +
86R ILE* 3.1 6.4 + - + +
88R GLU* 1.3 79.3 - - - +
90R ARG* 1.3 54.6 + - - +
91R PRO* 3.3 3.8 - - - -
92R THR* 3.1 10.8 + - - +
93R LEU* 2.7 51.0 + - + +
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Residues in contact with ARG 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R ILE* 3.0 30.0 + - - +
87R GLN* 3.4 14.8 - - - +
89R LEU* 1.3 75.4 - - - +
91R PRO* 1.4 69.7 - - + +
93R LEU* 3.7 25.8 - - - +
94R ASN* 2.8 52.0 + - - +
98R ILE 4.5 3.2 + - - -
100R THR* 4.2 5.9 + - - +
103R GLU* 3.1 35.1 + - - -
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Residues in contact with PRO 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87R GLN 4.2 2.7 - - - +
88R GLU 3.8 11.7 - - - +
89R LEU 3.4 3.6 - - - -
90R ARG* 1.4 95.4 - - + +
92R THR* 1.3 59.0 + - - +
94R ASN* 3.3 9.1 + - + +
95R GLU* 2.8 33.4 + - - +
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Residues in contact with THR 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49R ASP* 2.9 27.6 + - - +
52R LEU* 4.5 16.4 - - + -
53R ARG* 3.5 21.7 + - + +
88R GLU 5.5 0.5 + - - -
89R LEU* 3.1 18.0 + - - +
91R PRO* 1.3 77.1 - - - +
93R LEU* 1.3 64.9 - - - +
95R GLU* 4.2 5.6 - - - -
96R LEU* 3.0 53.6 + - + +
98R ILE* 5.0 0.2 - - + -
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Residues in contact with LEU 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52R LEU* 4.2 14.1 - - + -
68R LEU* 4.0 11.0 - - + -
86R ILE* 4.0 14.4 - - + +
89R LEU* 2.7 44.4 + - + +
90R ARG* 3.7 22.9 - - - +
91R PRO 3.3 0.2 - - - -
92R THR* 1.3 71.4 - - - +
94R ASN* 1.3 54.7 + - - +
97R GLY* 2.8 28.1 + - - -
98R ILE* 2.9 56.2 + - + +
100R THR* 4.0 24.2 - - + -
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Residues in contact with ASN 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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49Q SER* 4.2 4.7 + - - -
90R ARG* 2.8 50.4 + - - +
91R PRO* 3.5 7.0 - - + +
93R LEU* 1.3 75.6 - - - +
95R GLU* 1.3 66.7 + - - +
97R GLY* 3.3 11.4 + - - -
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Residues in contact with GLU 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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47Q SER* 5.4 2.3 + - - -
49Q SER* 4.5 3.8 + - - -
53R ARG* 3.4 36.4 + - - -
91R PRO* 2.8 22.7 + - - +
92R THR* 3.6 6.1 - - - +
94R ASN* 1.3 75.6 - - - +
96R LEU* 1.3 68.4 + - + +
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Residues in contact with LEU 96 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47Q SER* 4.9 1.4 + - - -
48Q TRP* 3.1 36.0 + - + +
49Q SER* 4.2 2.2 - - - -
52R LEU 4.2 19.7 - - - +
53R ARG* 4.2 22.4 - - + +
56R ARG* 4.5 25.6 + - + +
92R THR* 3.0 31.1 + - + +
95R GLU* 1.3 90.9 - - + +
97R GLY* 1.3 59.8 + - - +
98R ILE* 3.5 31.6 - - + -
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Residues in contact with GLY 97 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Q TRP* 3.5 8.7 - - - +
49Q SER* 3.4 23.3 - - - -
56Q LYS* 2.5 35.1 + - - -
61R PHE* 4.0 0.2 - - - -
93R LEU 2.8 9.4 + - - -
94R ASN* 3.3 8.3 + - - -
95R GLU 3.8 0.2 + - - -
96R LEU* 1.3 79.2 - - - +
98R ILE* 1.3 56.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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