Contacts of the helix formed by residues 75 - 90 (chain V) in PDB entry 3SDI
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 ARG 75 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223M LYS* 5.8 2.0 - - - +
105U TYR* 3.4 51.5 - - + +
143U GLU* 2.7 80.2 + - - +
41V ILE* 3.9 6.7 - - - +
63V ILE* 4.4 1.7 - - - +
72V ARG* 4.9 1.6 - - - +
73V GLU 4.0 7.8 + - - +
74V PRO* 1.3 77.5 - - - +
76V VAL* 1.3 65.5 + - - +
77V VAL* 4.3 15.9 - - + -
78V SER* 3.1 28.1 + - - +
79V ALA 3.5 4.0 + - - -
105V ASP* 3.3 22.8 - - + +
106V THR* 4.1 20.9 - - - +
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Residues in contact with VAL 76 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41V ILE* 3.8 18.6 - - + +
75V ARG* 1.3 66.3 - - - +
77V VAL* 1.3 57.5 + - - +
78V SER 2.8 11.5 + - - -
79V ALA* 3.1 4.8 + - - +
80V LEU* 2.9 21.0 + - - +
101V VAL* 4.1 20.6 - - + -
102V ALA* 4.8 0.4 - - - -
103V GLY* 3.7 40.2 - - - +
104V VAL 4.4 0.7 - - - +
105V ASP* 2.9 15.0 + - - +
109V HIS* 3.8 15.7 - - + +
111V PHE* 3.6 28.3 - - + -
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Residues in contact with VAL 77 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220M GLY 3.6 26.9 - - - +
221M THR* 4.1 13.4 - - + +
103U TYR 3.8 4.6 - - - +
104U GLY* 3.7 25.8 - - - +
105U TYR* 4.7 5.8 - - + +
75V ARG* 4.3 15.9 - - + -
76V VAL* 1.3 75.0 - - - +
78V SER* 1.3 56.6 + - - +
80V LEU* 3.7 9.9 - - + +
81V GLN* 3.1 28.4 + - - +
105V ASP* 4.7 1.0 + - - +
109V HIS* 4.9 12.1 - - + +
111V PHE* 4.1 13.9 - - + -
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Residues in contact with SER 78 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103U TYR* 2.5 35.3 + - - +
105U TYR* 3.5 19.8 - - - -
63V ILE* 3.8 16.8 - - - -
66V HIS* 4.7 3.2 - - - -
75V ARG* 3.1 15.8 + - - +
76V VAL 2.8 2.0 + - - -
77V VAL* 1.3 77.4 - - - +
79V ALA* 1.3 65.2 + - - -
80V LEU 3.1 0.9 - - - -
81V GLN* 4.0 0.6 - - - +
82V MET* 2.8 34.1 + - - +
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Residues in contact with ALA 79 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37V ILE* 4.2 35.9 - - + -
41V ILE* 4.4 10.8 - - + -
59V ILE* 4.2 11.7 - - + -
63V ILE* 3.9 6.4 - - + +
75V ARG 3.5 5.4 + - - +
76V VAL 3.1 9.8 + - - +
78V SER* 1.3 76.0 - - - +
80V LEU* 1.3 54.1 + - - +
82V MET* 3.8 0.7 - - - +
83V LEU* 2.8 44.2 + - + +
101V VAL* 4.4 4.5 - - + -
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Residues in contact with LEU 80 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219M TYR 4.1 6.3 - - - +
220M GLY* 3.5 33.4 - - - -
221M THR* 5.0 0.4 - - + +
76V VAL 2.9 14.8 + - - +
77V VAL* 3.7 9.6 - - - +
79V ALA* 1.3 76.4 - - - +
81V GLN* 1.3 64.3 + - - +
83V LEU* 3.7 1.3 - - - +
84V LYS* 2.8 36.1 + - - +
101V VAL* 3.9 6.4 - - + +
111V PHE* 3.3 44.0 - - + -
113V ILE* 3.3 29.0 - - + +
119V THR* 3.8 13.7 - - + +
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Residues in contact with GLN 81 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572 ASP* 3.5 26.9 + - - +
221M THR* 3.6 27.2 + - - +
100U ARG* 4.8 7.7 + - - +
101U TYR* 3.2 30.6 + - - +
102U LYS 3.7 15.9 - - - +
103U TYR 4.4 3.8 - - - -
104U GLY* 4.4 3.1 - - - +
77V VAL 3.1 14.5 + - - +
78V SER 3.3 2.0 + - - +
80V LEU* 1.3 82.4 - - - +
82V MET* 1.3 63.1 + - - +
84V LYS* 3.8 16.3 - - - +
85V GLN* 3.1 37.6 + - - +
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Residues in contact with MET 82 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102U LYS* 4.0 14.8 - - + +
103U TYR* 4.2 24.9 - - + +
59V ILE* 3.9 18.7 - - + +
62V ASN* 3.3 47.1 - - + +
63V ILE* 3.9 25.8 - - - -
66V HIS* 5.5 1.1 - - + -
78V SER 2.8 20.4 + - - +
79V ALA 3.9 0.7 - - - +
81V GLN* 1.3 76.0 - - - +
83V LEU* 1.3 63.0 + - - +
85V GLN* 3.9 4.0 - - - +
86V HIS* 3.0 27.0 + - - +
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Residues in contact with LEU 83 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37V ILE* 4.2 22.4 - - + -
55V VAL* 3.6 34.1 - - + +
56V THR* 5.1 2.0 - - - -
59V ILE* 3.6 28.3 - - + -
79V ALA* 2.8 30.4 + - + +
80V LEU* 3.7 3.1 - - - +
82V MET* 1.3 76.9 - - - +
84V LYS* 1.3 57.3 + - - +
86V HIS* 3.3 2.3 + - - +
87V LEU* 2.9 38.1 + - + +
99V LEU* 4.1 21.3 - - + -
101V VAL* 4.8 7.2 - - + -
113V ILE* 3.7 18.4 - - + -
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Residues in contact with LYS 84 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532 GLN* 2.8 33.4 + - + +
542 ALA* 5.6 6.1 - - + +
572 ASP* 4.1 16.4 + - - +
219M TYR* 3.5 20.0 - - - -
220M GLY* 6.4 0.2 - - - -
80V LEU* 2.8 20.8 + - - +
81V GLN* 3.8 22.9 - - - +
83V LEU* 1.3 74.8 - - - +
85V GLN* 1.3 67.9 + - + +
88V PHE* 3.0 30.6 + - + +
113V ILE* 4.4 7.8 - - - +
117V GLY* 3.5 24.3 - - - +
119V THR* 3.1 30.8 + - + -
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Residues in contact with GLN 85 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572 ASP* 4.9 3.0 + - - +
101U TYR* 3.2 63.6 + - - +
102U LYS* 4.2 16.3 - - - +
81V GLN* 3.1 32.3 + - - +
82V MET* 4.0 4.1 - - - +
84V LYS* 1.3 81.4 - - + +
86V HIS* 1.3 66.0 + - - +
88V PHE* 3.9 6.1 - - + +
89V LYS* 3.2 24.3 + - - +
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Residues in contact with HIS 86 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55V VAL* 3.3 32.4 - - + +
58V LEU* 3.9 22.4 - - + +
59V ILE* 4.5 13.2 - - + -
82V MET 3.0 18.2 + - - +
83V LEU 3.8 2.0 - - - +
85V GLN* 1.3 74.7 - - - +
87V LEU* 1.3 65.3 + - - +
89V LYS* 3.3 21.9 + - - +
90V TYR* 3.2 52.2 - + - -
95V ILE* 3.6 19.4 - - + +
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Residues in contact with LEU 87 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55V VAL* 4.1 16.2 - - + -
83V LEU* 2.9 19.8 + - + +
84V LYS 4.0 3.4 - - - +
86V HIS* 1.3 77.0 - - + +
88V PHE* 1.3 62.3 + - - +
90V TYR* 3.1 16.3 + - - +
91V GLN 3.5 6.8 + - - -
93V GLY 4.1 0.3 + - - -
95V ILE* 3.8 42.9 + - + +
97V ALA* 4.0 20.0 - - + +
99V LEU* 4.9 8.7 - - + -
113V ILE* 3.7 29.6 - - + -
114V HIS 3.9 9.2 - - - +
115V ALA 3.7 19.1 - - - +
116V HIS 4.3 0.2 - - - -
117V GLY* 4.2 5.4 - - - -
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Residues in contact with PHE 88 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502 ALA* 3.9 11.9 - - + -
512 ASP* 3.2 26.9 - - - -
542 ALA* 3.9 32.5 - - + -
552 ILE* 6.4 0.2 - - + -
582 ILE* 6.4 1.3 - - + -
952 LEU* 4.6 13.0 - - + -
84V LYS* 3.0 21.1 + - + +
85V GLN* 3.9 7.2 - - - +
86V HIS 3.3 0.2 - - - -
87V LEU* 1.3 75.2 - - - +
89V LYS* 1.3 67.4 + - - +
91V GLN* 3.0 51.1 + - - -
116V HIS 3.4 22.8 + - - +
117V GLY* 4.3 3.1 - - - +
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Residues in contact with LYS 89 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85V GLN 3.2 12.7 + - - +
86V HIS* 3.3 27.8 + - - +
88V PHE* 1.3 84.2 - - + +
90V TYR* 1.3 83.0 + - + +
91V GLN* 3.4 10.7 + - - +
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Residues in contact with TYR 90 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86V HIS* 3.2 43.1 - + - -
87V LEU 3.1 8.5 + - - +
88V PHE 3.1 1.2 - - - -
89V LYS* 1.3 101.5 + - + +
91V GLN* 1.3 67.1 + - - +
93V GLY 3.3 1.8 - - - -
94V HIS* 2.9 25.4 + + + +
95V ILE* 3.5 36.1 - - + +
92W PHE* 4.0 26.9 - + - -
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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
------------------------------------------------------------
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