Contacts of the helix formed by residues 86 - 95 (chain M) in PDB entry 1HNW
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 CYS 86 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81M LEU* 3.3 27.2 - - + +
84M ILE* 2.5 22.7 + - + +
85M GLY* 1.3 77.6 - - - +
87M TYR* 1.3 65.8 + - - +
88M ARG* 3.3 31.2 - - - -
89M GLY* 2.9 13.6 + - - -
90M LEU* 3.1 9.2 + - - +
3S ARG* 4.3 4.5 - - - -
69S HIS* 4.7 3.8 - - - -
73S GLU* 3.5 25.4 - - - -
74S PHE* 3.6 15.1 - - + -
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Residues in contact with TYR 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1320A C 3.5 22.2 - - - +
1321A C 3.2 42.6 + - - -
1322A C 4.1 6.9 + - - -
85M GLY 3.2 0.6 + - - -
86M CYS* 1.3 71.5 - - - +
88M ARG* 1.3 77.0 + - + +
90M LEU* 2.7 38.0 + - + +
91M ARG* 3.1 55.3 + - + +
98M VAL 5.0 7.7 + - - -
100M GLY* 5.9 2.2 - - - -
72S GLY 5.5 0.2 - - - +
73S GLU* 2.8 26.0 + - + +
76S PRO* 5.6 11.0 - - + -
77S THR 6.1 0.7 - - - -
78S ARG* 5.4 0.7 + - - -
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Residues in contact with ARG 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1309A G 3.2 33.6 + - - +
1310A G 3.0 31.7 + - - -
81M LEU* 3.6 25.0 - - + +
86M CYS* 3.3 11.8 - - - -
87M TYR* 1.3 84.7 - - + +
89M GLY* 1.3 63.4 + - - +
91M ARG* 3.3 22.7 - - - +
92M HIS* 3.6 10.9 - - + -
98M VAL* 3.2 23.4 - - + +
99M ARG* 5.2 0.6 - - - +
2S PRO* 3.8 20.4 - - - +
3S ARG* 3.3 36.4 - - - +
69S HIS* 5.7 1.0 - - - -
73S GLU* 4.8 1.7 + - + +
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Residues in contact with GLY 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81M LEU* 3.3 30.3 - - - +
82M MET* 4.0 8.4 - - - +
86M CYS* 2.9 12.1 + - - -
87M TYR 2.8 2.6 + - - -
88M ARG* 1.3 75.7 - - - +
90M LEU* 1.3 55.2 + - - +
91M ARG 3.0 1.6 - - - -
92M HIS* 2.6 32.5 + - - +
93M ARG* 3.2 10.0 + - - +
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Residues in contact with LEU 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84M ILE 5.8 0.2 - - - +
85M GLY* 3.7 16.2 - - - +
86M CYS 3.1 9.9 + - - +
87M TYR* 2.7 31.6 + - + +
89M GLY* 1.3 70.3 - - - +
91M ARG* 1.3 58.0 + - + +
93M ARG* 3.0 42.4 + - - +
94M ARG* 2.8 39.5 + - + +
73S GLU 5.6 0.4 - - - +
76S PRO* 4.8 18.4 - - + -
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Residues in contact with ARG 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1225A A 4.8 0.4 + - - -
1226A C 3.1 37.4 + - - -
87M TYR* 3.1 56.2 + - + +
88M ARG* 3.3 15.0 - - - +
90M LEU* 1.3 78.5 - - - +
92M HIS* 1.3 58.0 + - - +
94M ARG* 3.5 6.4 + - - +
95M GLY 2.8 23.6 + - - -
96M LEU* 3.0 52.9 + - - +
97M PRO 3.1 18.6 + - - +
98M VAL* 3.8 15.1 + - + -
103M THR* 3.5 11.1 - - - +
110M ARG* 4.5 0.2 - - - -
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Residues in contact with HIS 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1308A U 3.1 26.0 + - - -
1309A G 2.8 24.0 + - - -
78M ILE* 3.6 30.1 - - + +
81M LEU* 4.8 7.2 - - + +
82M MET* 3.3 20.6 - - + -
88M ARG* 3.6 22.0 + - + -
89M GLY* 2.6 17.1 + - - +
91M ARG* 1.3 74.2 - - - +
93M ARG* 1.3 57.6 + - - +
95M GLY* 2.8 20.1 + - - -
98M VAL* 3.5 14.1 - - + +
110M ARG* 3.0 24.7 + - - +
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Residues in contact with ARG 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82M MET* 2.5 56.9 + - + +
83M ASP* 3.7 14.3 + - - +
84M ILE 4.8 3.0 + - - -
85M GLY* 5.3 2.2 - - - -
89M GLY 3.9 3.6 - - - +
90M LEU* 3.0 40.4 + - - +
92M HIS* 1.3 78.9 - - - +
94M ARG* 1.3 64.4 + - + +
95M GLY* 3.1 1.6 + - - -
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Residues in contact with ARG 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1227A A 5.6 0.5 + - - -
90M LEU* 2.8 26.5 + - + +
91M ARG* 3.9 7.6 - - - +
93M ARG* 1.3 75.4 - - + +
95M GLY* 1.3 61.2 + - - +
96M LEU* 3.3 28.6 + - + +
80S TYR* 4.6 21.9 + - - +
81S ARG* 3.2 52.8 + - - +
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Residues in contact with GLY 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91M ARG 2.8 5.5 + - - -
92M HIS 2.8 16.2 + - - -
93M ARG 3.0 1.1 - - - -
94M ARG* 1.3 81.1 - - - +
96M LEU* 1.3 60.4 + - - +
110M ARG* 3.1 40.4 + - - +
111M LYS* 4.7 1.9 - - - -
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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
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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