Contacts of the helix formed by residues 96 - 109 (chain A) in PDB entry 1HE1
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 SER 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ALA* 1.3 72.5 - - - +
97A SER* 1.3 61.7 + - - +
98A ALA 3.1 0.7 - - - -
99A VAL* 2.9 37.6 - - - +
100A VAL* 3.5 5.5 + - - +
104D HIS* 5.2 7.7 - - - -
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Residues in contact with SER 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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95A ALA* 3.9 10.7 - - - +
96A SER* 1.3 81.9 + - - +
98A ALA* 1.3 59.6 + - - +
99A VAL 3.1 0.9 - - - -
100A VAL* 3.1 15.2 + - - +
101A PHE* 2.9 28.8 + - - +
69D PRO* 3.8 37.5 + - - +
70D LEU* 4.5 6.6 - - - +
73D PRO* 5.5 4.9 - - - +
104D HIS* 4.4 10.8 + - - -
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Residues in contact with ALA 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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95A ALA* 3.2 30.0 + - + +
96A SER 3.1 0.2 - - - -
97A SER* 1.3 82.6 + - - +
99A VAL* 1.3 56.3 + - + +
101A PHE* 3.6 8.5 + - - +
102A LYS* 3.0 27.0 + - - +
37C PHE* 5.7 0.2 - - - -
39C ASN* 5.0 14.3 + - - +
73D PRO* 6.5 1.3 - - - -
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Residues in contact with VAL 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 ALA 3.8 11.4 - - - +
96A SER* 2.9 25.4 - - - +
97A SER 3.1 0.2 - - - -
98A ALA* 1.3 77.4 - - + +
100A VAL* 1.3 66.8 + - + +
102A LYS* 3.7 10.8 - - + +
103A GLN* 2.9 32.6 + - + +
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Residues in contact with VAL 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 SER 3.7 14.4 - - - +
97A SER* 3.1 15.0 + - - +
99A VAL* 1.3 84.1 - - + +
101A PHE* 1.3 66.9 + - - +
103A GLN* 3.1 7.9 + - + +
104A MET* 2.9 35.6 + - + +
108B GLN* 5.0 10.8 - - + +
66D ARG 5.5 5.8 - - - +
70D LEU* 4.0 21.5 - - + -
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Residues in contact with PHE 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 SER 2.9 15.3 + - - +
98A ALA* 3.9 8.1 - - - +
100A VAL* 1.3 77.3 - - - +
102A LYS* 1.3 65.3 + - - +
104A MET* 3.0 18.3 + - + +
105A VAL* 2.9 52.6 + - + +
101B PHE* 3.5 38.4 - + - -
104B MET* 5.0 4.0 - - + -
37C PHE* 3.9 20.2 - + - -
56C TRP* 3.9 20.9 - + - -
70C LEU* 3.7 23.1 - - + -
70D LEU* 4.3 8.9 - - + +
73D PRO* 6.2 5.8 - - + -
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Residues in contact with LYS 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 ALA 3.0 19.1 + - - +
99A VAL* 3.7 10.3 - - + +
101A PHE* 1.3 76.0 - - - +
103A GLN* 1.3 61.6 - - - +
105A VAL* 3.3 2.4 + - - +
106A LEU* 2.9 48.7 + - + +
37C PHE* 3.9 28.3 - - + +
38C ASP* 3.0 36.5 + - - +
39C ASN* 4.0 17.0 + - - +
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Residues in contact with GLN 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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99A VAL* 2.9 19.3 + - + +
100A VAL* 3.4 7.9 - - + +
102A LYS* 1.3 81.1 - - - +
104A MET* 1.3 62.9 + - - +
106A LEU* 3.4 10.4 + - - +
107A GLN* 3.0 47.1 + - - +
157A ALA 2.9 28.5 + - - -
158A GLY* 4.5 4.9 - - - -
159A SER 5.7 1.2 + - - -
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Residues in contact with MET 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 VAL* 2.9 19.8 + - + +
101A PHE* 3.0 11.0 + - + +
103A GLN* 1.3 76.7 - - - +
105A VAL* 1.3 61.7 + - - +
107A GLN* 3.4 12.4 + - - +
108A GLN* 3.0 23.2 + - - +
101B PHE* 4.8 7.4 - - + -
104B MET* 3.7 54.3 - - + +
105B VAL* 4.0 14.8 - - + +
108B GLN* 3.5 29.4 - - + +
70D LEU* 3.8 34.3 - - + -
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Residues in contact with VAL 105 (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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101A PHE* 2.9 51.6 + - + +
102A LYS 3.6 7.4 - - - +
104A MET* 1.3 73.7 - - - +
106A LEU* 1.3 66.7 + - - +
108A GLN* 3.0 15.8 + - - +
109A ALA* 3.0 9.5 + - - +
104B MET* 4.2 7.0 - - + -
37C PHE* 3.6 36.3 - - + -
67C LEU* 3.6 25.7 - - + +
70C LEU* 4.3 15.7 - - + -
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Residues in contact with LEU 106 (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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102A LYS* 2.9 43.8 + - + +
103A GLN* 3.4 12.1 + - - +
105A VAL* 1.3 75.7 - - - +
107A GLN* 1.3 63.0 + - - +
109A ALA* 3.1 17.1 + - - +
110A LEU 3.6 4.3 + - - -
154A GLY* 4.8 6.5 - - - +
157A ALA* 3.7 33.4 - - + +
158A GLY* 3.8 21.9 - - - +
36C VAL* 3.9 31.0 - - + -
37C PHE* 4.4 17.9 - - + +
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Residues in contact with GLN 107 (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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103A GLN* 3.0 43.2 + - - +
104A MET* 3.7 7.7 + - - +
106A LEU* 1.3 76.8 - - - +
108A GLN* 1.3 63.1 + - - +
110A LEU* 3.1 21.6 + - + +
111A PRO* 4.1 2.1 - - - +
158A GLY 3.6 22.0 - - - +
160A GLN* 3.2 40.1 + - + +
108B GLN* 4.6 16.3 + - - +
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Residues in contact with GLN 108 (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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104A MET 3.0 13.0 + - - +
105A VAL* 3.0 15.1 + - - +
107A GLN* 1.3 78.5 - - - +
109A ALA* 1.3 60.1 + - - +
111A PRO* 3.3 14.7 - - - +
112A MET* 3.6 15.5 - - + +
100B VAL* 4.3 15.0 - - + +
104B MET* 3.8 32.9 - - + +
107B GLN* 5.1 9.7 - - - +
67C LEU* 4.0 14.1 - - + -
70C LEU* 4.5 3.6 - - + -
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Residues in contact with ALA 109 (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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105A VAL 3.0 5.4 + - - +
106A LEU* 3.4 11.4 - - + +
107A GLN 3.1 0.8 - - - -
108A GLN* 1.3 77.8 - - - +
110A LEU* 1.3 64.6 + - - +
111A PRO* 3.4 0.9 - - - -
112A MET* 2.8 21.0 + - - +
113A THR* 3.0 15.9 + - + +
154A GLY* 5.9 1.3 - - - -
36C VAL* 3.7 17.7 - - + -
64C TYR* 4.6 6.3 - - + -
67C LEU* 3.7 32.1 - - + +
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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