Contacts of the helix formed by residues 80 - 93 (chain A) in PDB entry 2IHD
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ARG* 4.3 8.5 - - + +
74A LEU* 3.6 24.5 + - + -
75A LYS* 3.6 42.7 - - + +
78A PHE* 4.1 5.7 - - - -
79A SER* 1.3 83.0 + - - +
81A GLU* 1.3 63.9 + - - +
82A ASN 3.1 0.2 - - - -
83A LEU* 3.0 6.3 + - + +
84A GLU* 2.9 52.3 + - + +
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Residues in contact with GLU 81 (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 PHE 3.8 14.3 - - - +
79A SER* 3.4 20.3 + - - -
80A GLU* 1.3 88.0 + - - +
82A ASN* 1.3 63.7 + - - +
84A GLU* 3.6 12.5 - - - +
85A PHE* 2.9 32.1 + - - +
112A PHE* 4.0 1.6 - - - -
119A ARG* 3.6 30.7 - - + +
120A GLU 3.7 22.0 - - - +
121A VAL* 3.6 7.8 - - + +
122A ASN* 5.7 2.4 + - - -
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Residues in contact with ASN 82 (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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74A LEU* 5.1 0.6 - - + +
79A SER* 3.1 28.7 + - - +
81A GLU* 1.3 80.8 - - - +
83A LEU* 1.3 57.7 + - - +
85A PHE* 3.6 2.6 + - - +
86A TRP* 3.0 26.7 + - - +
121A VAL* 3.8 24.3 - - - +
122A ASN 4.7 1.7 + - - -
150A VAL* 4.0 15.2 - - + +
153A LEU* 4.5 24.0 - - - +
154A MET* 3.8 27.8 - - + +
158A SER* 5.3 3.8 + - - -
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Residues in contact with LEU 83 (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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61A LEU* 3.9 27.8 - - + -
67A VAL* 4.0 13.9 - - + +
70A PHE* 4.3 11.2 - - + -
71A ARG* 3.6 45.3 - - + +
74A LEU* 3.7 15.0 - - + -
79A SER 4.3 0.2 + - - -
80A GLU* 3.0 8.7 + - + +
82A ASN* 1.3 77.4 - - - +
84A GLU* 1.3 63.4 + - + +
86A TRP* 3.2 4.4 + - + -
87A LEU* 2.9 55.4 + - + +
154A MET* 3.8 15.0 - - + -
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Residues in contact with GLU 84 (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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71A ARG* 6.0 7.1 - - + +
75A LYS* 5.2 4.9 - - - -
80A GLU* 2.9 41.3 + - + +
81A GLU* 3.6 13.3 + - - +
83A LEU* 1.3 77.4 - - + +
85A PHE* 1.3 56.8 + - - +
87A LEU* 3.9 8.3 - - + +
88A ALA* 2.9 29.8 + - - +
112A PHE* 3.8 5.8 - - + -
119A ARG* 3.0 45.0 + - - +
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Residues in contact with PHE 85 (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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81A GLU 2.9 18.1 + - - +
82A ASN 3.8 1.8 - - - +
84A GLU* 1.3 73.2 - - - +
86A TRP* 1.3 67.3 + - - +
88A ALA* 3.2 1.2 + - - +
89A CYS* 3.0 42.8 + - - -
108A ILE* 3.8 15.7 - - + -
112A PHE* 3.6 38.5 - + + -
113A VAL* 3.8 19.3 - - + -
121A VAL* 3.8 13.0 - - + -
143A PHE* 4.2 5.4 - + - -
146A ALA* 3.8 44.2 - - + -
147A GLN* 3.9 4.9 - - - -
150A VAL* 3.6 26.2 - - + -
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Residues in contact with TRP 86 (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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1A CL 3.5 14.3 - - - +
58A ASP* 5.0 3.1 - - - -
61A LEU* 3.8 43.7 - - + -
82A ASN 3.0 19.3 + - - +
83A LEU* 3.2 5.6 + - + +
85A PHE* 1.3 78.4 - - - +
87A LEU* 1.3 81.2 + - + +
89A CYS* 3.3 1.7 + - - +
90A GLU* 3.1 54.8 + - + +
147A GLN* 3.2 53.7 + - + +
150A VAL* 4.1 7.2 - - + -
151A HIS* 3.6 21.0 - + + -
154A MET* 3.8 14.1 - - + -
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Residues in contact with LEU 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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67A VAL* 4.0 18.2 - - + -
71A ARG* 3.3 30.3 - - - +
83A LEU* 2.9 39.9 + - + +
84A GLU* 3.9 7.0 - - + +
86A TRP* 1.3 98.5 - - + +
88A ALA* 1.3 61.3 + - - +
90A GLU* 3.2 7.5 + - + +
91A GLU* 3.0 27.9 + - - +
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Residues in contact with ALA 88 (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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84A GLU 2.9 18.7 + - - +
85A PHE 3.5 5.2 - - - +
87A LEU* 1.3 75.5 - - - +
89A CYS* 1.3 57.8 + - - +
91A GLU* 3.3 7.3 + - - +
92A PHE* 2.8 28.9 + - - +
104A LYS* 5.5 0.2 - - - +
108A ILE* 3.7 22.3 - - + +
112A PHE* 4.1 19.3 - - + -
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Residues in contact with CYS 89 (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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85A PHE* 3.0 52.5 + - - -
86A TRP 3.5 8.3 - - - +
87A LEU 3.2 0.2 - - - -
88A ALA* 1.3 72.9 - - - +
90A GLU* 1.3 65.3 + - - +
92A PHE* 3.2 10.1 + - + +
93A LYS* 3.1 27.8 + - + +
108A ILE* 4.8 2.9 - - - -
143A PHE* 3.6 25.1 - - + -
147A GLN* 3.5 27.6 - - - +
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Residues in contact with GLU 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 TRP* 3.1 53.3 + - + +
87A LEU* 3.2 12.1 + - + +
89A CYS* 1.3 77.0 - - - +
91A GLU* 1.3 61.2 + - - +
93A LYS* 2.8 50.8 + - - +
94A LYS* 3.8 19.3 + - - +
147A GLN* 2.8 13.3 + - - +
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Residues in contact with GLU 91 (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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87A LEU 3.0 12.3 + - - +
88A ALA* 3.6 10.3 - - - +
89A CYS 3.3 0.2 - - - -
90A GLU* 1.3 74.0 - - - +
92A PHE* 1.3 67.7 + - - +
94A LYS* 3.0 31.0 + - + +
95A THR* 4.0 3.8 + - - -
104A LYS* 5.1 14.2 - - + +
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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
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88A ALA 2.8 17.6 + - - +
89A CYS* 3.2 9.8 + - - +
91A GLU* 1.3 77.1 - - - +
93A LYS* 1.3 59.2 + - + +
95A THR* 2.7 34.1 + - - -
101A LEU* 3.4 45.5 - - + -
104A LYS* 4.2 16.5 - - + +
105A ALA* 3.8 17.5 - - + -
108A ILE* 3.8 22.9 - - + -
139A SER 3.4 25.6 - - - -
140A LEU* 3.5 23.9 - - + +
142A CYS* 4.2 1.6 - - + -
143A PHE* 3.8 23.3 - + + -
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Residues in contact with LYS 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 CYS* 3.1 15.0 + - + +
90A GLU* 2.8 41.8 + - - +
91A GLU 3.2 0.8 - - - -
92A PHE* 1.3 77.6 - - + +
94A LYS* 1.3 58.5 + - + +
95A THR 3.3 2.3 + - - +
140A LEU* 4.0 40.0 - - + +
144A ASP* 4.3 15.5 + - - +
147A GLN* 3.1 19.9 + - - +
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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