Contacts of the helix formed by residues 98 - 113 (chain A) in PDB entry 1A8H
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 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A THR 3.7 4.4 + - - +
97A GLU* 1.3 71.0 - - - +
99A ARG* 1.3 60.5 + - - +
100A HIS 3.1 0.2 + - - -
101A LYS* 3.0 35.4 + - - +
102A LYS* 2.9 34.1 + - + +
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Residues in contact with ARG 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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91A ASP* 2.6 43.0 + - - -
92A PHE 3.5 7.9 + - - -
93A ILE* 3.6 17.2 - - + +
97A GLU* 2.5 41.8 + - + +
98A GLU* 1.3 78.4 - - - +
100A HIS* 1.3 63.9 - - - +
102A LYS* 3.8 6.6 + - - +
103A VAL* 3.3 27.9 + - - +
236A SER* 4.2 10.2 + - - +
237A ALA* 3.8 18.8 + - - +
239A ASP* 4.5 16.4 + - - +
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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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93A ILE* 4.5 7.8 - - + +
94A ARG 4.1 12.6 - - - +
95A THR* 3.3 34.5 - - + +
97A GLU* 3.2 8.9 + - + +
98A GLU 3.1 0.8 - - - -
99A ARG* 1.3 81.0 - - - +
101A LYS* 1.3 66.1 + - - +
103A VAL 3.2 2.6 + - - -
104A VAL* 3.0 36.9 + - + +
214A ILE* 4.0 3.4 - - + -
229A ASP* 2.8 42.6 + - - -
232A LEU 3.9 1.1 - - - -
233A ASN* 3.6 26.0 - - + +
236A SER* 3.0 31.5 + - - -
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Residues in contact with LYS 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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95A THR 5.5 1.3 - - - +
96A THR 5.6 1.1 - - - +
97A GLU 3.1 12.7 + - - +
98A GLU* 3.0 34.1 - - - +
100A HIS* 1.3 75.3 - - - +
102A LYS* 1.3 64.0 + - - +
104A VAL* 3.2 2.1 + - - +
105A GLN* 3.0 50.2 + - + +
214A ILE* 4.1 30.4 - - + +
215A PRO* 4.0 29.9 - - - +
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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 GLU* 2.9 17.3 + - + +
99A ARG* 3.8 8.7 - - - +
100A HIS 3.2 0.2 - - - -
101A LYS* 1.3 80.2 - - - +
103A VAL* 1.3 60.1 + - + +
105A GLN* 3.7 5.6 + - - +
106A LEU* 3.1 32.8 + - + +
241A PRO* 6.5 1.6 - - + -
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Residues in contact with VAL 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 ARG 3.3 15.9 + - - +
100A HIS 3.2 1.6 + - - +
102A LYS* 1.3 77.7 - - + +
104A VAL* 1.3 60.1 + - - +
106A LEU* 3.3 6.7 + - - +
107A VAL* 2.9 33.3 + - + +
232A LEU* 4.7 4.7 - - + +
235A VAL* 3.8 24.9 - - + -
236A SER* 3.1 34.8 - - - +
239A ASP* 5.2 2.5 - - - -
240A TYR* 3.8 15.3 - - + +
241A PRO* 4.4 18.8 - - + -
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Residues in contact with VAL 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 49.3 + - + +
101A LYS 3.7 3.6 - - - +
103A VAL* 1.3 74.4 - - - +
105A GLN* 1.3 58.0 + - - +
107A VAL* 3.3 2.6 + - - +
108A LEU* 2.9 51.5 + - + +
214A ILE* 4.2 19.1 - - + -
224A THR* 4.1 10.8 - - + +
228A PHE 3.4 26.9 - - - +
229A ASP* 4.1 2.2 - - - +
232A LEU* 3.6 12.9 - - + +
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Residues in contact with GLN 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 LYS* 3.0 45.7 + - - +
102A LYS* 4.0 5.2 - - - +
104A VAL* 1.3 74.9 - - - +
106A LEU* 1.3 58.2 + - - +
108A LEU* 3.3 5.0 + - - +
109A LYS* 2.9 33.2 + - - +
214A ILE* 3.7 14.4 - - + +
215A PRO* 2.8 32.7 + - - +
217A PRO* 3.6 26.6 - - + +
220A GLU* 5.8 1.2 + - - -
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A LYS* 3.1 23.1 + - + +
103A VAL* 3.5 7.4 - - - +
104A VAL 3.2 0.2 - - - -
105A GLN* 1.3 77.4 - - - +
107A VAL* 1.3 61.5 + - + +
109A LYS* 3.6 13.2 + - + +
110A LYS* 3.2 23.6 + - + +
240A TYR* 4.4 11.9 - - + -
241A PRO* 3.5 34.1 - - + -
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Residues in contact with VAL 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 VAL* 2.9 24.4 + - + +
106A LEU* 1.3 73.2 - - - +
108A LEU* 1.3 59.7 + - - +
110A LYS* 3.8 5.1 - - - +
111A VAL* 3.0 32.9 + - + +
228A PHE* 4.1 13.2 - - + -
232A LEU* 3.7 33.4 - - + -
240A TYR* 4.0 26.7 - - + +
272A MET* 5.4 0.4 - - + +
276A ALA* 3.9 24.0 - - + -
278A ILE* 4.5 8.1 - - + -
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Residues in contact with LEU 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 VAL* 2.9 34.2 + - + +
105A GLN* 3.5 5.4 - - - +
107A VAL* 1.3 75.5 - - - +
109A LYS* 1.3 60.2 + - - +
111A VAL* 3.3 2.4 + - - -
112A TYR* 2.8 31.7 + - - +
117A ILE* 3.8 4.3 - - + +
203A ILE* 3.9 23.3 - - + -
215A PRO 4.9 1.3 - - - +
216A LEU* 3.9 12.1 - - + -
217A PRO* 4.1 11.4 - - + -
218A TRP* 3.3 20.0 - - + -
224A THR* 3.3 28.0 - - + +
228A PHE* 3.7 32.1 - - + -
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Residues in contact with LYS 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 GLN 2.9 16.9 + - - +
106A LEU* 3.9 13.9 - - + +
108A LEU* 1.3 75.9 - - - +
110A LYS* 1.3 57.8 + - - +
112A TYR* 3.7 3.7 - - + +
113A GLU* 2.9 62.1 + - + +
217A PRO* 4.2 21.1 - - + -
218A TRP* 4.0 9.8 - - + -
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Residues in contact with LYS 110 (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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106A LEU* 3.2 19.2 + - + +
107A VAL* 3.8 6.5 - - - +
109A LYS* 1.3 79.1 - - - +
111A VAL* 1.3 61.1 + - - +
113A GLU* 4.0 9.8 - - - +
114A ALA* 3.2 23.8 + - - +
240A TYR* 5.5 3.1 - - - +
275A ALA 3.7 18.2 - - - -
276A ALA* 3.2 32.3 - - + +
277A GLY* 5.2 1.1 - - - -
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Residues in contact with VAL 111 (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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107A VAL* 3.0 26.5 + - + +
108A LEU 3.9 2.7 - - - +
110A LYS* 1.3 77.6 - - + +
112A TYR* 1.3 65.8 + - - +
114A ALA* 3.4 9.5 + - - +
116A ASP* 3.2 39.3 + - + +
117A ILE* 3.9 16.8 - - + -
161A PHE* 4.0 14.4 - - + -
228A PHE* 4.4 11.9 - - + -
272A MET 4.9 0.7 - - - +
275A ALA* 4.0 8.1 - - + +
276A ALA* 3.9 29.8 - - + +
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Residues in contact with TYR 112 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A LEU 2.8 17.8 + - - +
109A LYS* 3.3 5.6 + - + +
111A VAL* 1.3 77.7 - - - +
113A GLU* 1.3 70.3 + - + +
115A GLY* 3.1 18.7 + - - -
117A ILE* 3.7 31.0 + - + +
118A TYR* 6.0 0.7 - - - -
159A TYR* 5.1 3.6 - + - -
218A TRP* 3.4 71.2 - + + +
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Residues in contact with GLU 113 (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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109A LYS* 2.9 53.3 + - + +
110A LYS* 4.1 8.0 - - - +
112A TYR* 1.3 83.4 - - + +
114A ALA* 1.3 59.5 + - - +
115A GLY* 3.0 6.8 + - - -
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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