Contacts of the helix formed by residues 93 - 104 (chain A) in PDB entry 2HPD
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 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A ARG* 2.8 45.9 + - - -
84A ASP* 3.9 10.9 - - - +
89A SER* 3.4 6.2 - - - -
90A TRP* 3.1 44.6 + - + +
91A THR 3.8 3.3 - - - +
92A HIS* 1.3 77.6 - - - +
94A LYS* 1.3 63.8 + - - +
95A ASN* 4.3 3.8 - - + +
96A TRP* 3.1 23.7 + - + +
97A LYS* 3.8 4.3 + - - +
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Residues in contact with LYS 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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92A HIS 3.6 2.4 + - - -
93A GLU* 1.3 72.1 - - - +
95A ASN* 1.3 64.7 + - - +
96A TRP 3.4 0.2 + - - -
97A LYS* 3.5 20.3 + - + +
98A LYS* 3.2 35.0 + - + +
245A THR* 4.5 13.7 - - + -
247A GLU* 2.9 41.2 + - - -
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Residues in contact with ASN 95 (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 ASP* 2.9 36.6 + - + +
93A GLU* 3.3 3.9 - - + +
94A LYS* 1.3 79.0 - - - +
96A TRP* 1.4 66.5 + - - +
98A LYS* 3.5 27.1 + - - -
99A ALA* 3.1 23.2 + - - +
249A LEU* 5.0 1.6 - - - +
250A ASP* 4.1 16.5 + - - +
253A ASN* 3.9 24.0 + - - +
257A GLN* 5.0 0.2 + - - -
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Residues in contact with TRP 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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84A ASP 5.7 0.7 - - - -
86A LEU* 3.4 24.6 - - + +
89A SER* 3.3 27.6 + - - +
90A TRP 3.4 18.4 - - - +
91A THR* 3.6 31.2 - - + +
93A GLU* 3.1 9.9 + - - +
95A ASN* 1.4 75.6 - - - +
97A LYS* 1.3 80.7 + - + +
99A ALA 3.7 0.2 - - - -
100A HIS* 2.8 75.3 + + + +
397A GLN* 3.4 39.9 - - + -
398A ARG* 3.2 22.5 - - - +
472A HEM 2.9 19.7 + - - -
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Residues in contact with LYS 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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91A THR 3.9 9.9 - - - +
92A HIS* 3.7 28.5 + - - +
93A GLU 3.8 10.8 + - - +
94A LYS* 3.8 16.7 - - + +
95A ASN 3.5 0.2 - - - -
96A TRP* 1.3 90.1 - - + +
98A LYS* 1.3 58.2 + - - +
100A HIS* 3.8 1.5 - - - +
101A ASN* 3.0 40.0 + - - +
242A ASP* 5.2 0.4 - - - +
244A GLU* 4.4 21.8 - - - +
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Residues in contact with LYS 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 LYS* 3.2 24.7 + - + +
95A ASN* 3.5 24.7 + - - +
97A LYS* 1.3 78.8 - - - +
99A ALA* 1.3 57.7 + - - +
101A ASN* 3.8 1.6 - - - +
102A ILE* 3.1 37.6 + - + +
242A ASP* 3.8 23.6 - - + +
245A THR* 3.8 20.6 - - + +
247A GLU* 3.3 30.1 + - + +
248A PRO 2.8 25.6 + - - +
249A LEU* 4.1 15.8 - - + +
250A ASP* 4.5 7.1 + - - -
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Residues in contact with ALA 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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86A LEU* 3.4 13.9 - - + -
95A ASN 3.1 18.6 + - - +
98A LYS* 1.3 73.6 - - - +
100A HIS* 1.3 66.7 + - - +
102A ILE* 3.2 1.2 + - - -
103A LEU* 2.8 33.8 + - + +
249A LEU* 3.8 19.8 - - + +
257A GLN* 3.4 30.5 - - - +
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Residues in contact with HIS 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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86A LEU* 3.6 9.7 - - + +
96A TRP* 2.8 60.3 + + + +
97A LYS* 3.8 3.1 - - - +
99A ALA* 1.3 72.7 - - - +
101A ASN* 1.3 69.2 + - - +
104A LEU* 3.0 68.7 + - + +
397A GLN* 3.8 27.6 + - + +
401A ILE* 4.7 8.3 - - + +
472A HEM 4.6 4.2 + - - -
384B ALA* 5.3 7.1 + - - +
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Residues in contact with ASN 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 LYS* 3.0 24.3 + - - +
98A LYS 3.8 1.1 - - - +
100A HIS* 1.3 87.0 - - - +
102A ILE* 1.3 62.4 + - - +
104A LEU* 4.4 4.1 - - - +
105A PRO* 3.7 13.5 - - - +
242A ASP* 2.8 30.3 + - - +
243A PRO* 4.1 17.5 - - + +
244A GLU* 3.5 33.6 + - - +
386B PRO* 6.0 2.8 - - - +
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Residues in contact with ILE 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 LYS* 3.1 22.4 + - + +
99A ALA* 3.9 3.6 - - - +
101A ASN* 1.3 75.7 - - - +
103A LEU* 1.3 72.5 + - + +
105A PRO* 3.4 17.5 - - - +
106A SER* 4.4 5.0 + - - -
236A HIS* 4.3 10.3 - - + +
237A MET* 4.8 8.1 - - - +
240A GLY* 4.2 26.5 - - - +
241A LYS 3.8 7.2 - - - +
242A ASP* 3.6 37.7 - - + +
243A PRO* 5.4 0.7 - - - -
247A GLU 4.3 2.9 - - - +
249A LEU* 3.8 29.8 - - + +
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Residues in contact with LEU 103 (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 LEU* 3.8 23.1 - - + -
99A ALA* 2.8 30.8 + - + +
102A ILE* 1.3 79.6 - - + +
104A LEU* 1.3 64.6 + - - +
106A SER* 2.9 22.0 + - - +
107A PHE* 3.4 11.7 + - + -
233A LEU* 4.3 23.1 - - + +
236A HIS* 5.5 1.8 - - + -
237A MET* 3.8 35.9 - - + +
249A LEU* 5.1 1.6 - - + -
257A GLN* 4.5 5.6 - - - -
261A PHE* 3.9 20.0 - - + -
401A ILE* 3.9 15.3 - - + -
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Residues in contact with LEU 104 (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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100A HIS* 3.0 52.9 + - + +
101A ASN* 4.4 4.5 - - - +
103A LEU* 1.3 75.3 - - - +
105A PRO* 1.3 69.5 - - + +
107A PHE* 3.1 11.8 + - - +
108A SER* 3.6 8.0 + - - -
401A ILE* 4.1 18.5 - - + +
365B THR 5.0 4.7 - - - +
366B ILE* 5.5 9.0 - - + +
384B ALA 5.5 2.9 - - - +
386B PRO* 4.2 25.6 - - + -
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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