Contacts of the helix formed by residues 98 - 112 (chain A) in PDB entry 1S89
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 ASN 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A HIS* 4.3 1.6 + - - -
67A PRO* 3.9 21.9 - - + +
71A ASP* 2.9 23.2 + - - +
96A VAL* 3.3 18.0 - - - +
97A PRO* 1.3 80.4 - - - +
99A ASP* 1.3 62.2 + - - +
100A PRO* 3.3 2.7 - - - -
101A ASP* 3.2 12.8 + - - +
102A VAL* 3.0 29.1 + - - +
201A PGA 3.4 22.1 + - - +
107F ARG* 3.7 26.2 - - - +
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Residues in contact with ASP 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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96A VAL* 3.3 27.2 + - + +
97A PRO 3.1 1.6 + - - +
98A ASN* 1.3 77.0 - - - +
100A PRO* 1.3 73.4 - - + +
102A VAL* 3.2 5.7 + - - +
103A LYS* 3.0 56.9 + - - +
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Residues in contact with PRO 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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97A PRO 3.7 9.6 - - - +
98A ASN 3.5 1.8 - - - -
99A ASP* 1.3 96.9 - - + +
101A ASP* 1.3 66.4 + - - +
103A LYS* 3.4 2.2 + - + -
104A ALA* 2.8 32.7 + - - +
100F PRO* 3.5 28.6 - - + +
103F LYS* 3.8 20.0 - - + +
104F ALA* 3.9 11.7 - - - +
107F ARG* 4.4 7.9 - - + -
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Residues in contact with ASP 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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66A GLY 4.5 3.5 - - - +
69A GLY* 5.1 0.7 - - - -
71A ASP* 3.6 25.9 - - + +
72A GLN* 3.3 25.0 + - + +
98A ASN* 3.2 9.4 + - + +
100A PRO* 1.3 78.5 - - - +
102A VAL* 1.3 58.2 + - - +
104A ALA* 3.4 3.1 + - - +
105A LEU* 2.9 30.3 + - - +
72F GLN* 5.2 1.0 - - - +
104F ALA* 3.6 20.2 - - - +
107F ARG* 2.7 46.8 + - - -
108F LEU* 4.4 1.6 - - - +
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Residues in contact with VAL 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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19A HIS* 3.5 28.7 - - + +
71A ASP* 4.1 3.1 - - - +
88A PHE* 3.6 29.1 - - + -
90A TRP* 4.3 15.5 - - + -
96A VAL* 4.2 4.0 - - + -
98A ASN* 3.0 26.3 + - - +
99A ASP* 3.2 9.6 + - - +
101A ASP* 1.3 76.1 - - - +
103A LYS* 1.3 74.0 + - - +
105A LEU* 3.2 5.8 + - - +
106A LEU* 3.1 32.7 + - + +
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Residues in contact with LYS 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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90A TRP* 4.6 21.3 - - - -
99A ASP* 3.0 51.3 + - - +
100A PRO* 3.9 4.5 - - + +
102A VAL* 1.3 83.2 - - + +
104A ALA* 1.3 57.6 + - - +
106A LEU* 3.3 12.7 + - + +
107A ARG* 2.9 29.5 + - - +
90B TRP* 5.3 1.6 - - - -
103B LYS* 3.9 42.2 - - + -
100F PRO* 3.9 17.7 - - + +
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Residues in contact with ALA 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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72A GLN* 6.1 0.2 - - + -
100A PRO 2.8 23.3 + - - +
101A ASP* 3.6 7.4 - - - +
103A LYS* 1.3 72.7 - - - +
105A LEU* 1.3 61.9 + - - +
107A ARG* 3.3 5.0 + - - +
108A LEU* 3.1 16.1 + - - +
72F GLN* 2.9 31.7 + - - +
100F PRO* 4.0 2.4 - - - +
101F ASP* 3.7 34.2 - - - +
104F ALA* 4.6 2.7 - - + -
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Residues in contact with LEU 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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17A VAL* 5.2 4.9 - - + -
71A ASP* 3.7 28.9 - - + +
74A VAL* 4.0 11.7 - - + -
75A GLY* 3.6 33.2 - - - +
78A ILE* 3.8 17.3 - - + -
86A LEU* 4.3 13.0 - - + -
88A PHE* 4.1 25.6 - - + -
101A ASP 2.9 17.2 + - - +
102A VAL* 3.2 5.6 + - - +
104A ALA* 1.3 77.8 - - - +
106A LEU* 1.3 62.1 + - - +
108A LEU* 3.3 3.0 + - + +
109A ALA* 3.1 20.8 + - - +
72F GLN* 3.9 6.0 - - - +
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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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86A LEU* 4.8 3.6 - - + -
88A PHE* 4.2 17.0 - - + -
90A TRP* 4.1 28.3 - - + +
102A VAL* 3.1 28.4 + - + +
103A LYS* 3.3 13.0 + - + +
105A LEU* 1.3 74.0 - - - +
107A ARG* 1.3 66.0 + - - +
109A ALA* 3.4 4.5 + - - +
110A THR* 3.0 27.7 + - - +
116A VAL* 4.1 17.9 - - + -
118A THR* 4.0 22.7 - - + -
90B TRP* 4.6 7.0 - - + -
106B LEU* 6.4 2.2 - - + -
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Residues in contact with ARG 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 LYS 2.9 18.1 + - - +
104A ALA* 3.5 4.0 - - - +
105A LEU 3.2 0.2 - - - -
106A LEU* 1.3 77.6 - - - +
108A LEU* 1.3 69.6 + - - +
110A THR* 3.2 4.3 + - - -
111A VAL* 2.9 40.8 + - - +
90B TRP* 3.8 27.3 - - + -
92B PRO* 3.1 31.3 + - + +
93B LEU* 3.8 4.6 - - - +
66F GLY 4.0 2.6 + - - -
67F PRO* 3.0 36.6 + - - +
97F PRO* 4.3 15.4 - - - +
98F ASN* 3.8 13.2 - - - +
100F PRO* 4.5 7.4 - - + -
101F ASP* 2.8 43.0 + - - -
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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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75A GLY* 3.6 26.0 - - - +
78A ILE* 4.5 4.3 - - + -
79A SER* 4.5 1.3 - - - -
104A ALA 3.1 9.8 + - - +
105A LEU* 3.8 4.7 - - + +
106A LEU 3.3 0.2 - - - -
107A ARG* 1.3 87.7 - - - +
109A ALA* 1.3 62.0 + - - +
111A VAL* 4.2 4.9 - - + -
112A TRP* 2.8 49.8 + - + +
67F PRO 4.2 2.7 - - - +
68F MET* 3.7 27.1 - - - +
69F GLY* 3.7 20.9 - - - +
72F GLN* 2.9 39.5 - - + +
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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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78A ILE* 4.4 8.2 - - + +
86A LEU* 3.9 16.6 - - + -
105A LEU 3.1 17.4 + - - +
106A LEU* 3.7 7.4 - - - +
107A ARG 3.3 0.2 - - - -
108A LEU* 1.3 76.2 - - - +
110A THR* 1.3 61.3 + - - +
112A TRP 3.7 0.2 + - - -
113A ASN 3.2 15.9 + - - -
114A ILE* 3.4 17.6 + - + +
116A VAL* 3.4 26.9 - - + -
119B ASN* 3.4 11.2 + - - -
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Residues in contact with THR 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 3.0 14.4 + - - -
107A ARG 3.4 9.0 - - - -
109A ALA* 1.3 75.1 - - - +
111A VAL* 1.3 65.6 + - - +
113A ASN* 3.2 13.3 + - - +
116A VAL* 5.2 0.4 - - - +
90B TRP* 3.6 29.4 + - + +
92B PRO* 3.9 21.7 - - + +
118B THR* 3.5 36.0 + - - +
119B ASN* 4.0 14.6 - - + +
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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 ARG* 2.9 40.2 + - - +
108A LEU* 3.6 7.9 - - + +
110A THR* 1.3 78.3 - - - +
112A TRP* 1.3 74.4 + - + +
113A ASN* 3.2 6.2 + - - +
141A PRO* 3.7 18.0 - - + +
92B PRO* 3.4 28.9 - - + -
93B LEU* 4.1 12.1 - - + -
67F PRO 4.6 3.6 - - - +
68F MET* 4.1 25.6 - - + -
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Residues in contact with TRP 112 (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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6A ARG* 5.6 3.0 + - - -
78A ILE* 4.0 17.0 - - + +
79A SER* 3.4 42.2 - - - -
81A GLY* 6.0 1.3 - - - -
108A LEU* 2.8 42.8 + - + +
109A ALA 3.9 0.4 - - - +
111A VAL* 1.3 75.6 - - + +
113A ASN* 1.3 69.9 + - - +
114A ILE* 3.4 12.8 + - + +
138A ILE* 4.0 0.7 - - - +
140A ILE* 3.9 34.6 - - + +
141A PRO* 4.1 30.1 - - + -
143A TYR* 4.6 13.9 - + + -
64F LEU* 4.5 6.1 - - + -
68F MET* 3.0 56.9 + - + -
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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