Contacts of the helix formed by residues 75 - 90 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2231 LYS* 5.6 2.8 - - - +
105G TYR* 3.5 51.8 - - + +
143G GLU* 2.7 77.4 + - - +
41H ILE* 3.8 7.1 - - - +
63H ILE* 4.3 1.6 - - - +
72H ARG* 5.1 1.8 - - - +
73H GLU 3.6 7.6 + - - +
74H PRO* 1.3 76.5 - - - +
76H VAL* 1.3 65.1 + - - +
77H VAL* 4.1 12.3 - - + +
78H SER* 3.0 29.7 + - - +
79H ALA 3.4 7.8 + - - -
105H ASP* 3.3 20.3 - - + +
106H THR* 3.8 26.4 - - - +
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Residues in contact with VAL 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H ILE* 3.9 19.7 - - + +
75H ARG* 1.3 71.2 - - - +
77H VAL* 1.3 56.3 + - - +
78H SER 3.1 0.2 - - - -
79H ALA* 3.1 4.6 + - - +
80H LEU* 2.9 27.3 + - - +
101H VAL* 4.0 22.4 - - + +
103H GLY* 3.7 40.2 - - - +
104H VAL 4.3 0.9 - - - +
105H ASP* 2.9 14.2 + - + +
109H HIS* 3.8 18.2 - - + -
111H PHE* 3.7 26.7 - - + -
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Residues in contact with VAL 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2201 GLY 3.7 23.8 - - - +
2211 THR* 4.1 14.4 - - + +
103G TYR 3.7 3.4 - - - +
104G GLY* 3.5 28.5 - - - +
105G TYR* 4.7 2.5 - - + -
75H ARG* 4.1 22.0 - - + +
76H VAL* 1.3 75.4 - - - +
78H SER* 1.3 59.8 + - - +
80H LEU* 3.8 7.9 - - - +
81H GLN* 3.1 27.5 + - - +
105H ASP* 4.6 1.0 + - - +
106H THR* 6.2 0.4 - - - +
109H HIS* 4.9 12.8 - - + +
111H PHE* 4.3 11.0 - - + -
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Residues in contact with SER 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G TYR* 2.6 33.7 + - - +
105G TYR* 3.3 23.1 - - - -
63H ILE* 3.9 14.4 - - - -
66H HIS* 4.7 3.8 - - - -
75H ARG* 3.0 16.1 + - - +
77H VAL* 1.3 75.5 - - - +
79H ALA* 1.3 67.5 + - - +
81H GLN* 4.0 0.3 - - - +
82H MET* 3.0 35.8 + - - +
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Residues in contact with ALA 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ILE* 4.2 31.9 - - + -
41H ILE* 4.4 14.4 - - + -
59H ILE* 4.3 10.1 - - + -
63H ILE* 4.0 7.7 - - + +
75H ARG 3.4 5.7 + - - +
76H VAL 3.1 10.9 + - - +
78H SER* 1.3 79.2 - - - +
80H LEU* 1.3 61.7 + - - +
82H MET* 4.0 1.2 - - - +
83H LEU* 3.1 31.6 + - - +
101H VAL* 4.7 4.7 - - + -
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Residues in contact with LEU 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2191 TYR 4.3 0.2 - - - +
2201 GLY* 3.8 31.6 - - - -
2211 THR* 5.3 1.6 - - + -
76H VAL 2.9 15.9 + - - +
77H VAL* 3.8 8.7 - - - +
78H SER 3.2 0.2 - - - -
79H ALA* 1.3 75.7 - - - +
81H GLN* 1.3 62.1 + - - +
82H MET 3.1 0.3 + - - -
83H LEU* 3.2 3.4 + - - +
84H LYS* 2.8 38.2 + - - +
101H VAL* 4.2 5.2 - - + +
111H PHE* 3.3 42.0 - - + -
113H ILE* 3.5 24.9 - - + +
119H THR* 3.6 26.5 - - + +
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Residues in contact with GLN 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2211 THR* 4.0 19.5 + - - +
100G ARG* 4.6 10.7 + - - +
101G TYR* 2.9 32.3 + - - +
102G LYS 3.4 15.9 - - - +
103G TYR 4.3 4.5 - - - -
104G GLY* 4.2 3.1 - - - +
77H VAL 3.1 16.7 + - - +
78H SER 3.5 2.4 + - - +
80H LEU* 1.3 81.4 - - - +
82H MET* 1.3 61.4 + - - +
84H LYS* 3.4 20.5 - - - +
85H GLN* 3.1 39.0 + - - +
57N ASP* 4.0 22.3 + - - +
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Residues in contact with MET 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G LYS* 4.0 14.4 - - + +
103G TYR* 3.8 30.1 - - + +
59H ILE* 3.8 18.7 - - + +
62H ASN* 3.4 42.8 - - + +
63H ILE* 3.9 22.7 - - + -
66H HIS* 5.4 1.1 - - + -
78H SER 3.0 22.8 + - - +
79H ALA 4.0 1.6 - - - +
81H GLN* 1.3 73.1 - - - +
83H LEU* 1.3 66.6 + - - +
85H GLN* 3.3 6.8 + - - +
86H HIS* 3.0 25.8 + - - +
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Residues in contact with LEU 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ILE* 4.5 18.2 - - + -
55H VAL* 3.5 45.1 - - + +
56H THR* 5.2 2.5 - - - +
59H ILE* 3.7 18.6 - - + +
79H ALA* 3.1 27.7 + - + +
80H LEU 3.6 2.9 - - - +
82H MET* 1.3 76.4 - - - +
84H LYS* 1.3 57.1 + - - +
86H HIS* 3.3 3.9 + - - +
87H LEU* 2.8 40.5 + - + +
99H LEU* 4.0 14.8 - - + -
101H VAL* 4.7 7.6 - - + -
113H ILE* 3.6 25.4 - - + -
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Residues in contact with LYS 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2191 TYR* 3.4 19.6 - - - -
80H LEU* 2.8 22.7 + - - +
81H GLN* 3.4 26.0 - - - +
83H LEU* 1.3 74.6 - - - +
85H GLN* 1.3 67.0 + - + +
88H PHE* 2.9 31.8 + - + +
113H ILE* 4.5 7.4 - - + +
117H GLY* 3.7 22.6 + - - +
119H THR* 3.1 33.2 + - + -
53N GLN* 2.9 32.7 + - + +
54N ALA* 5.9 3.6 - - + +
57N ASP* 3.7 18.4 + - - +
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Residues in contact with GLN 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G TYR* 3.2 61.5 + - - +
102G LYS* 3.8 22.5 - - - +
81H GLN* 3.1 30.2 + - - +
82H MET* 3.9 4.9 - - - +
83H LEU 3.2 0.2 - - - -
84H LYS* 1.3 79.8 - - + +
86H HIS* 1.3 65.6 + - - +
88H PHE* 3.8 5.6 - - - +
89H LYS* 3.1 24.3 + - - +
57N ASP* 5.1 3.2 + - - +
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Residues in contact with HIS 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H VAL* 3.5 29.7 - - + +
58H LEU* 3.6 28.1 - - + +
59H ILE* 4.4 10.1 - - + -
82H MET 3.0 17.0 + - - +
83H LEU 3.6 3.8 - - - +
85H GLN* 1.3 74.6 - - - +
87H LEU* 1.3 66.5 - - + +
89H LYS* 3.0 42.7 + - - +
90H TYR* 3.4 29.7 + + - -
95H ILE* 3.6 22.1 - - + +
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Residues in contact with LEU 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H VAL* 4.0 14.6 - - + -
83H LEU* 2.8 26.5 + - + +
84H LYS 4.1 2.5 - - - +
86H HIS* 1.3 73.4 - - + +
88H PHE* 1.3 64.9 + - - +
90H TYR* 3.1 15.7 + - - +
91H GLN 3.4 6.4 + - - -
93H GLY 4.0 0.9 + - - -
95H ILE* 3.7 42.9 - - + +
97H ALA* 4.0 27.8 - - + +
99H LEU* 4.8 8.5 - - + -
113H ILE* 3.9 27.1 - - + -
114H HIS 4.1 3.8 - - - +
115H ALA* 3.7 18.4 - - - +
117H GLY* 4.2 5.8 - - - -
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Residues in contact with PHE 88 (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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84H LYS* 2.9 20.6 + - + +
85H GLN* 3.8 6.7 - - - +
87H LEU* 1.3 78.2 - - - +
89H LYS* 1.3 61.1 + - - +
91H GLN* 2.8 47.2 + - - -
116H HIS 3.3 23.0 + - - +
117H GLY* 4.4 4.3 - - - +
50N ALA* 3.7 23.3 - - + -
51N ASP* 3.5 27.6 - - - -
54N ALA* 3.8 21.5 - - + -
58N ILE* 6.5 0.4 - - + -
95N LEU* 4.7 10.5 - - + -
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Residues in contact with LYS 89 (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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85H GLN 3.1 13.0 + - - +
86H HIS* 3.0 32.8 + - - +
88H PHE* 1.3 80.6 - - - +
90H TYR* 1.3 89.5 + - + +
91H GLN* 3.4 10.4 + - - +
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Residues in contact with TYR 90 (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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86H HIS* 3.4 30.1 + + - -
87H LEU 3.1 9.2 + - - +
88H PHE 3.1 1.4 - - - -
89H LYS* 1.3 102.2 - - + +
91H GLN* 1.3 69.2 + - - +
93H GLY 2.8 5.0 + - - -
94H HIS* 3.0 21.9 + + + -
95H ILE* 3.6 35.2 - - + +
92I PHE* 4.1 28.9 - + - -
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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