Contacts of the helix formed by residues 98 - 112 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B HIS* 3.7 10.9 + - - -
66B GLY 3.4 0.2 - - - -
67B PRO* 3.2 33.1 - - + +
71B ASP* 3.0 22.1 + - - -
96B VAL* 3.6 15.1 - - - +
97B PRO* 1.3 75.3 - - - +
99B ASP* 1.3 62.3 + - - +
100B PRO* 3.3 3.4 - - - -
101B ASP* 3.1 24.5 + - - +
102B VAL* 3.0 19.8 + - - +
202B PGA 3.3 13.2 + - - +
107E ARG* 3.9 14.8 - - - +
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Residues in contact with ASP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ALA* 6.1 0.4 - - - -
96B VAL* 3.5 31.4 + - + +
97B PRO 3.1 2.2 + - - +
98B ASN* 1.3 76.2 - - - +
100B PRO* 1.4 72.4 - - + +
102B VAL* 3.1 7.3 + - - +
103B LYS* 3.0 54.7 + - - +
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Residues in contact with PRO 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PRO 3.8 6.7 - - - +
98B ASN 3.5 0.9 - - - -
99B ASP* 1.4 96.1 - - + +
101B ASP* 1.3 66.5 + - - +
103B LYS* 3.4 1.7 + - + -
104B ALA* 2.9 30.8 + - - +
100E PRO* 3.5 29.8 - - + +
103E LYS* 3.8 20.6 - - + +
104E ALA* 3.9 6.3 - - - +
107E ARG* 4.4 12.1 - - + -
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Residues in contact with ASP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLY 4.6 2.9 - - - +
69B GLY* 5.5 1.0 - - - -
71B ASP* 3.7 26.9 - - + +
72B GLN* 3.1 24.8 + - + +
98B ASN* 3.1 12.0 + - + +
100B PRO* 1.3 82.4 - - - +
102B VAL* 1.3 57.8 + - - +
104B ALA* 3.8 2.5 - - - +
105B LEU* 2.9 30.3 + - - +
72E GLN* 5.2 1.2 - - - +
104E ALA* 3.8 15.7 - - - +
107E ARG* 2.8 46.9 + - - -
108E LEU* 4.6 0.3 - - - +
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B HIS* 3.4 32.8 - - + +
71B ASP* 4.7 3.8 - - - +
88B PHE* 3.8 26.0 - - + -
90B TRP* 4.4 15.5 - - + -
96B VAL* 4.4 0.7 - - + -
98B ASN* 3.0 21.5 + - - +
99B ASP* 3.2 12.3 - - - +
101B ASP* 1.3 77.3 - - - +
103B LYS* 1.3 78.3 + - + +
105B LEU* 3.2 5.5 + - - +
106B LEU* 3.1 31.4 + - + +
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TRP* 5.2 1.9 - - - -
103A LYS* 3.9 41.1 - - - +
90B TRP* 4.3 26.6 - - - -
99B ASP* 3.0 46.9 + - - +
100B PRO* 4.6 1.1 - - + -
102B VAL* 1.3 86.8 - - + +
104B ALA* 1.3 57.7 + - - +
106B LEU* 3.5 11.0 + - + +
107B ARG* 3.0 28.9 + - - +
100E PRO* 3.8 21.8 - - + +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLN* 6.1 0.4 - - + -
100B PRO 2.9 18.4 + - - +
101B ASP* 3.8 6.5 - - - +
103B LYS* 1.3 74.9 - - - +
105B LEU* 1.3 64.7 + - - +
107B ARG* 3.4 3.0 + - - +
108B LEU* 3.1 15.1 + - - +
72E GLN* 3.0 25.4 + - - +
100E PRO* 3.8 3.5 - - - +
101E ASP* 3.6 42.5 - - - +
104E ALA* 4.6 3.1 - - + -
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 4.9 5.2 - - + -
71B ASP* 3.4 28.5 - - + +
74B VAL* 3.9 17.0 - - + -
75B GLY* 3.4 36.8 - - - +
78B ILE* 4.0 7.2 - - + -
86B LEU* 4.2 14.6 - - + -
88B PHE* 3.9 27.6 - - + -
101B ASP 2.9 17.7 + - - +
102B VAL 3.5 4.9 - - - +
104B ALA* 1.3 78.2 - - - +
106B LEU* 1.3 62.0 + - - +
108B LEU* 3.3 3.3 + - - +
109B ALA* 3.1 22.4 + - - +
72E GLN* 4.1 4.7 + - - +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TRP* 4.5 7.9 - - + -
106A LEU* 6.4 2.0 - - + -
86B LEU* 4.4 4.5 - - + -
88B PHE* 4.1 19.3 - - + -
90B TRP* 4.2 26.7 - - + +
102B VAL* 3.1 24.7 + - + +
103B LYS* 4.0 11.4 - - + +
105B LEU* 1.3 79.3 - - - +
107B ARG* 1.3 60.8 + - - +
109B ALA* 3.5 4.2 + - - +
110B THR* 2.9 29.2 + - - +
116B VAL* 4.2 17.5 - - + -
118B THR* 3.9 23.3 - - + -
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TRP* 3.7 21.5 - - + -
92A PRO* 3.0 37.6 + - + +
93A LEU* 3.8 8.1 - - - +
103B LYS 3.0 18.6 + - - +
104B ALA* 3.6 3.4 - - - +
106B LEU* 1.3 77.2 - - - +
108B LEU* 1.3 69.7 + - - +
110B THR* 3.1 5.7 + - - -
111B VAL* 2.9 35.6 + - - +
66E GLY 4.0 1.6 + - - -
67E PRO* 2.9 36.8 + - - +
97E PRO* 3.7 17.9 - - - +
98E ASN* 3.8 12.0 - - - +
100E PRO* 4.5 6.3 - - + -
101E ASP* 2.8 43.8 + - - -
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLY* 3.7 24.7 - - - +
78B ILE* 4.6 4.0 - - + -
79B SER* 4.4 2.2 - - - -
104B ALA 3.1 7.3 + - - +
105B LEU* 3.8 4.3 - - - +
107B ARG* 1.3 96.1 - - - +
109B ALA* 1.3 57.4 + - - +
111B VAL* 3.1 5.9 + - + -
112B TRP* 2.9 49.1 + - + +
67E PRO 4.0 3.1 - - - +
68E MET* 3.7 28.3 - - - +
69E GLY* 3.6 18.8 - - - +
72E GLN* 2.9 38.4 - - + +
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ASN* 3.3 16.5 + - - -
78B ILE* 4.3 9.1 - - + +
86B LEU* 3.9 18.2 - - + -
105B LEU 3.1 15.9 + - - +
106B LEU* 3.8 6.5 - - - +
107B ARG 3.3 0.2 - - - -
108B LEU* 1.3 77.3 - - - +
110B THR* 1.3 60.9 + - - +
112B TRP 3.8 0.2 + - - -
113B ASN 3.4 10.0 + - - -
114B ILE* 3.4 19.5 + - + +
116B VAL* 3.6 23.8 - - + -
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Residues in contact with THR 110 (chain B).
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* 3.5 24.4 - - + +
92A PRO* 3.8 26.4 - - + +
118A THR* 3.5 35.3 + - - +
119A ASN* 3.9 13.2 - - + +
106B LEU 2.9 16.0 + - - -
107B ARG 3.1 10.7 + - - -
108B LEU 3.1 0.2 - - - -
109B ALA* 1.3 75.9 - - - +
111B VAL* 1.3 66.3 + - - +
113B ASN* 3.2 13.5 + - - +
116B VAL* 5.6 0.6 - - - +
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PRO* 3.5 27.6 - - + +
93A LEU* 4.3 11.0 - - + -
107B ARG* 2.9 37.4 + - - +
108B LEU* 3.4 13.5 - - + +
110B THR* 1.3 76.9 - - - +
112B TRP* 1.3 75.3 + - + +
113B ASN* 3.1 5.9 + - - +
141B PRO* 3.5 20.7 - - + +
67E PRO 4.5 1.3 - - - +
68E MET* 4.0 23.6 - - - -
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Residues in contact with TRP 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ARG* 5.8 2.0 + - - -
78B ILE* 4.2 17.7 - - + +
79B SER* 3.5 40.0 - - - -
81B GLY* 6.3 0.4 - - - -
108B LEU* 2.9 41.9 + - + +
109B ALA 4.0 0.9 - - - +
111B VAL* 1.3 77.9 - - + +
113B ASN* 1.3 70.2 + - - +
114B ILE* 3.3 11.3 + - + +
138B ILE* 4.1 0.9 - - - +
140B ILE* 3.8 36.7 - - + +
141B PRO* 3.8 28.7 - - + -
143B TYR* 4.5 16.2 - + + -
64E LEU* 4.5 6.7 - - + -
68E MET* 3.1 53.9 + - + -
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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