Contacts of the helix formed by residues 86 - 102 (chain A) in PDB entry 2HW6
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 HIS 86 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ALA 3.2 2.6 + - - -
85A GLY* 1.3 77.2 - - - +
87A SER* 1.3 58.8 + - - +
88A ARG 3.6 1.3 - - - -
89A SER* 3.9 15.7 - - - +
90A ARG* 3.1 60.1 + - - +
225A GLU* 3.7 27.4 + - - +
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ILE* 3.6 8.5 - - - +
81A GLU 2.7 27.5 + - - -
82A LYS* 3.5 11.2 - - - -
84A ALA 3.4 16.2 + - - -
85A GLY 3.2 0.6 - - - -
86A HIS* 1.3 73.9 - - - +
88A ARG* 1.3 68.6 + - - +
91A VAL* 2.9 30.7 + - - +
120A PHE* 3.8 8.4 - - - -
226A VAL* 3.6 22.7 - - - +
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Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS* 3.5 49.9 + - + +
86A HIS 3.6 0.2 - - - -
87A SER* 1.3 78.7 - - - +
89A SER* 1.3 58.4 + - - +
92A PHE* 3.2 27.5 + - - +
115A GLU* 5.9 0.9 - - - +
117A ASP 4.3 5.9 + - - -
120A PHE* 3.8 25.7 - - + -
43B LYS* 5.6 3.0 - - - +
45B GLU* 3.0 35.9 + - - -
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Residues in contact with SER 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A HIS* 3.5 22.5 + - - +
88A ARG* 1.3 77.7 - - - +
90A ARG* 1.3 66.4 + - - +
92A PHE* 3.4 5.0 + - - +
93A ARG* 3.2 48.1 + - - +
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A HIS* 3.1 49.8 + - + +
89A SER* 1.3 82.3 + - - +
91A VAL* 1.3 56.8 + - - +
93A ARG* 3.3 26.5 + - - +
94A GLU* 3.0 28.7 + - - +
225A GLU* 3.3 30.1 + - - +
226A VAL* 2.8 49.6 + - + -
227A VAL* 5.0 2.6 - - - +
228A GLU* 3.6 32.6 + - + +
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 4.2 17.5 - - + -
87A SER* 2.9 27.8 + - - +
90A ARG* 1.3 74.0 - - - +
92A PHE* 1.3 59.5 + - - +
94A GLU* 3.2 10.4 + - + +
95A VAL* 2.9 34.6 + - + +
113A PHE* 4.5 0.9 - - + -
120A PHE* 3.9 39.0 - - + -
122A LEU* 4.0 25.1 - - + -
226A VAL* 4.2 13.5 - - + -
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Residues in contact with PHE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ARG 3.2 21.3 + - - +
89A SER* 3.4 4.9 + - - +
91A VAL* 1.3 77.2 - - - +
93A ARG* 1.3 71.9 + - + +
95A VAL* 3.6 5.1 + - + +
96A GLU* 3.0 64.7 + - + +
113A PHE* 6.1 5.2 - + - -
120A PHE* 5.5 3.0 - - + -
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Residues in contact with ARG 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A SER* 3.2 40.9 + - - +
90A ARG* 3.3 27.5 + - - +
92A PHE* 1.3 86.2 - - + +
94A GLU* 1.3 64.6 + - - +
96A GLU* 3.7 6.1 + - - +
97A THR* 3.1 27.4 + - - -
228A GLU* 3.0 27.1 + - - +
230A PHE 4.6 1.5 - - - +
231A THR* 6.1 1.8 - - - +
232A ASP* 5.9 5.1 - - + +
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LYS* 5.1 2.5 + - - +
90A ARG 3.0 17.9 + - - +
91A VAL* 3.2 12.0 + - + +
93A ARG* 1.3 74.8 - - - +
95A VAL* 1.3 60.5 + - + +
97A THR* 3.4 2.4 + - - -
98A LEU* 2.9 45.5 + - + +
122A LEU* 5.0 9.8 - - + +
124A PHE* 5.7 0.7 - - - -
191A ASP* 2.6 42.6 - - - +
226A VAL* 5.3 5.0 - - - +
227A VAL 4.4 8.5 - - - +
229A VAL 3.7 20.3 + - - +
230A PHE* 3.8 16.2 - - + -
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Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 2.9 20.5 + - + +
92A PHE* 4.0 5.6 - - + +
94A GLU* 1.3 73.7 - - - +
96A GLU* 1.3 70.7 + - - +
98A LEU* 2.9 18.7 + - - +
99A TYR* 2.9 48.6 + - + +
110A LEU* 4.1 7.0 - - + -
113A PHE* 3.5 40.4 - - + -
122A LEU* 4.1 21.8 - - + -
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 3.0 53.5 + - + +
93A ARG* 3.8 7.2 - - - +
95A VAL* 1.3 79.3 - - - +
97A THR* 1.3 63.5 + - - +
99A TYR* 3.4 35.9 + - - +
100A GLN* 3.4 14.6 + - - +
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Residues in contact with THR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ARG 3.1 15.1 + - - -
94A GLU 3.7 2.7 - - - -
95A VAL 3.1 0.2 - - - -
96A GLU* 1.3 78.6 - - - +
98A LEU* 1.3 58.9 + - - +
100A GLN* 3.0 32.3 + - - +
101A CYS* 3.4 13.8 + - - -
166A ILE* 3.8 29.6 - - + -
230A PHE* 3.4 38.5 + - + +
232A ASP* 3.9 22.3 + - - +
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLU* 2.9 42.5 + - + +
95A VAL 2.9 5.8 + - - +
97A THR* 1.3 71.8 - - - +
99A TYR* 1.3 65.3 + - - +
101A CYS* 3.3 6.6 + - + +
102A GLN* 3.3 22.2 + - - +
107A ILE* 4.5 12.8 - - + -
108A LEU 4.6 8.5 - - - +
110A LEU* 4.0 21.2 + - + +
122A LEU* 4.3 9.6 - - + -
124A PHE* 4.0 28.3 - - + -
191A ASP* 6.0 0.2 - - + -
230A PHE* 3.9 37.9 - - + -
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Residues in contact with TYR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A VAL* 2.9 41.3 + - + +
96A GLU* 3.5 30.1 - - - +
98A LEU* 1.3 76.6 - - - +
100A GLN* 1.3 63.3 + - + +
102A GLN* 3.0 40.4 - - - +
110A LEU* 4.0 16.2 - - + -
112A GLU* 6.2 0.9 - - - -
113A PHE* 3.7 21.9 + - + +
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Residues in contact with GLN 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLU* 3.4 20.5 + - - +
97A THR* 3.0 22.8 + - - +
99A TYR* 1.3 77.9 - - + +
101A CYS* 1.3 58.9 + - - +
102A GLN 3.7 4.3 + - - +
160A PHE* 3.6 14.4 - - - -
164A LYS* 3.8 33.4 + - + +
166A ILE* 4.6 14.9 - - + +
232A ASP* 4.6 13.8 + - - +
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Residues in contact with CYS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A THR* 3.6 21.8 - - - -
98A LEU* 3.3 15.2 + - + +
99A TYR 3.2 1.0 - - - -
100A GLN* 1.3 76.0 - - - +
102A GLN* 1.3 67.1 + - - +
103A GLY 3.3 0.2 + - - -
104A ASN* 3.1 25.9 + - - +
107A ILE* 3.9 26.4 - - + +
160A PHE* 3.8 14.4 - - + -
161A LEU* 3.7 30.5 - - - -
166A ILE* 4.8 4.3 - - - -
230A PHE* 4.5 4.7 - - - -
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Residues in contact with GLN 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU 3.3 10.2 + - - +
99A TYR* 3.0 43.9 + - - +
100A GLN 4.1 5.9 - - - +
101A CYS* 1.3 76.0 - - - +
103A GLY* 1.3 58.5 + - - +
104A ASN 3.8 0.5 + - - -
107A ILE 5.9 0.2 - - - -
109A GLU* 3.9 31.4 - - + +
110A LEU 3.4 20.1 + - - +
111A ILE 5.3 2.6 + - - -
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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