Contacts of the strand formed by residues 97 - 109 (chain B) in PDB entry 3DOY
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 LYS 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B PHE* 4.2 11.9 - - + -
87B TRP* 3.6 34.8 - - + +
93B ILE* 3.6 25.8 - - + +
94B ALA 3.5 1.2 + - - +
95B LYS 3.4 0.2 - - - -
96B THR* 1.3 95.0 - - - +
98B ILE* 1.3 62.5 + - - +
131B MET* 5.7 2.6 - - - -
155B ILE* 4.4 9.9 - - + -
156B ALA 3.2 16.5 - - - +
157B GLU* 2.7 27.4 + - - +
158B ARG* 2.9 30.7 + - - +
2009B BEN 3.0 16.6 - - + -
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Residues in contact with ILE 98 (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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59A PHE* 4.7 4.3 - - + -
3001A 2BE 3.3 58.3 - - + +
22B PRO* 4.3 7.6 - - + -
97B LYS* 1.3 76.0 - - - +
99B VAL* 1.3 66.7 + - - +
100B TYR* 3.8 8.6 + - + +
154B MET 3.4 2.9 - - - +
155B ILE* 3.6 0.2 - - - -
156B ALA* 2.8 49.3 + - + +
157B GLU 4.1 11.4 - - - +
158B ARG* 4.3 10.1 - - - +
2009B BEN 2.8 37.9 - - + +
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Residues in contact with VAL 99 (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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23B HIS* 5.5 0.3 - - - -
79B GLY* 4.0 25.8 - - - +
82B ALA* 5.4 1.6 - - + -
83B PHE* 4.9 2.7 - - + -
98B ILE* 1.3 75.3 - - - +
100B TYR* 1.3 57.3 + - - +
101B PHE* 4.4 9.2 - - + -
153B ALA* 3.7 28.9 - - + -
154B MET 3.4 4.9 - - - +
155B ILE* 3.5 33.9 - - + -
2009B BEN 3.1 55.2 + - + +
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Residues in contact with TYR 100 (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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108A LYS* 6.2 0.4 - - - -
109A PHE 5.7 1.3 - - - -
3001A 2BE 3.5 67.3 - + + +
98B ILE* 4.6 12.6 - - + -
99B VAL* 1.3 75.9 - - - +
101B PHE* 1.3 73.0 + - - +
102B MET* 4.0 20.7 - - + +
153B ALA* 3.5 1.7 - - - -
154B MET* 3.0 68.4 + - + +
156B ALA* 4.6 11.0 - - + -
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Residues in contact with PHE 101 (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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109A PHE* 3.2 35.3 - - + +
3001A 2BE 5.0 1.6 - - - +
75B ALA* 3.2 45.8 - - + -
76B GLN* 5.3 0.2 - - - -
78B GLY* 4.9 2.5 - - - -
79B GLY* 4.2 7.9 - - - -
99B VAL* 4.4 12.6 - - + -
100B TYR* 1.3 86.3 - - - +
102B MET* 1.3 60.8 + - - +
103B THR 4.3 6.1 - - - +
104B ILE* 5.1 2.9 - - + -
135B VAL* 5.0 5.2 - - + -
151B LEU* 3.5 39.0 - - + -
152B LYS 3.8 12.3 - - - -
153B ALA* 3.5 24.7 - - + -
2009B BEN 5.7 2.2 - - - -
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Residues in contact with MET 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LYS* 3.3 32.2 - - - +
109A PHE* 2.9 33.1 + - - -
100B TYR* 4.0 14.4 - - + +
101B PHE* 1.3 75.2 - - - +
103B THR* 1.3 61.9 + - - +
132B ILE* 4.7 15.0 - - + -
152B LYS* 2.9 35.1 + - - +
153B ALA 4.3 7.4 - - - +
154B MET* 3.6 44.2 - - + -
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Residues in contact with THR 103 (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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107A VAL 3.1 13.5 - - - +
108A LYS* 3.9 22.9 - - + -
109A PHE* 5.3 0.7 - - - -
101B PHE* 4.3 2.9 - - - -
102B MET* 1.3 83.9 + - - +
104B ILE* 1.3 76.0 + - - +
105B ASP* 5.8 2.8 - - - +
151B LEU* 3.6 1.7 - - - +
152B LYS* 3.1 61.0 + - - +
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Residues in contact with ILE 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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68A VAL* 4.6 10.5 - - + -
71A VAL* 6.2 0.7 - - + -
104A ILE* 5.5 1.3 - - + -
106A LYS 3.9 0.2 + - - -
107A VAL* 3.1 46.2 + - + +
109A PHE* 3.8 30.5 - - + -
71B VAL* 4.0 26.7 - - + -
75B ALA* 5.9 1.3 - - + -
101B PHE* 5.1 5.4 - - + -
103B THR* 1.3 83.1 - - - +
105B ASP* 1.3 65.0 + - - +
107B VAL* 3.5 25.4 - - + -
149B ALA* 5.1 0.4 - - + -
150B GLU 3.3 9.9 - - - +
151B LEU* 4.3 15.9 - - + -
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Residues in contact with ASP 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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104A ILE 4.5 0.4 - - - -
105A ASP* 3.3 10.0 - - - +
106A LYS* 2.7 37.8 + - - +
103B THR* 5.8 3.4 - - - +
104B ILE* 1.3 76.2 - - - +
106B LYS* 1.3 100.4 + - + +
107B VAL* 3.1 7.3 + - - +
150B GLU* 2.7 36.3 + - + +
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Residues in contact with LYS 106 (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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104A ILE 3.9 0.2 + - - -
105A ASP* 3.3 16.9 + - - +
105B ASP* 1.3 98.6 + - - +
107B VAL* 1.3 61.4 + - - +
108B LYS* 3.7 24.0 + - - +
148B GLU* 3.4 13.5 - - - +
149B ALA* 3.6 5.4 - - - -
150B GLU* 3.8 33.7 - - + +
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Residues in contact with VAL 107 (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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103A THR* 3.3 6.2 - - - -
104A ILE* 3.0 45.7 + - + +
105A ASP* 4.7 0.7 - - - +
71B VAL* 4.1 12.6 - - + -
104B ILE* 3.5 32.5 - - + -
105B ASP 3.6 7.9 - - - +
106B LYS* 1.3 75.8 - - - +
108B LYS* 1.3 72.8 + - - +
109B PHE* 3.7 34.5 - - + -
147B ALA* 6.1 0.4 - - + -
148B GLU 3.2 8.3 - - - +
149B ALA* 3.6 11.7 - - + -
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Residues in contact with LYS 108 (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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102A MET 3.5 8.1 - - - +
103A THR* 3.9 15.0 - - + +
105A ASP* 4.9 3.0 + - - -
106B LYS* 3.7 36.2 + - - +
107B VAL* 1.3 79.8 + - - +
109B PHE* 1.3 66.3 + - - +
110B ARG* 4.1 17.8 + - + +
147B ALA* 3.2 7.8 - - - +
148B GLU* 3.1 56.5 + - + +
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Residues in contact with PHE 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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101A PHE* 3.4 54.1 - + + +
102A MET* 3.1 16.9 + - - +
103A THR 5.2 0.2 - - - -
104A ILE* 3.9 17.7 - - + -
67B GLY* 3.1 45.3 - - - -
68B VAL 4.3 0.2 - - - -
70B ILE* 4.8 7.4 - - + -
71B VAL* 4.1 7.9 - - + -
107B VAL* 3.7 24.5 - - + -
108B LYS* 1.3 74.3 - - - +
110B ARG* 1.3 61.8 + - - +
111B ILE 5.3 2.9 - - - +
146B VAL 3.7 3.8 - - - +
147B ALA* 4.0 19.1 - - + -
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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