Contacts of the strand formed by residues 144 - 157 (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 144 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B ILE* 4.3 20.4 - - + -
140B GLN* 3.1 7.0 - - - -
141B VAL 3.0 33.1 + - - +
142B ASP* 3.0 37.1 + - + +
143B GLY* 1.3 81.7 - - - +
145B VAL* 1.3 62.9 + - - +
146B VAL* 3.4 2.1 + - + +
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Residues in contact with VAL 145 (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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110B ARG* 3.9 32.0 - - - +
111B ILE* 3.8 14.0 - - - +
138B THR* 4.0 24.5 - - + +
139B ALA 3.7 4.3 - - - -
140B GLN* 4.1 11.0 - - + +
143B GLY 4.1 1.1 + - - +
144B LYS* 1.3 71.2 - - - +
146B VAL* 1.3 61.1 + - - +
147B ALA 3.4 25.8 - - - +
148B GLU* 4.4 3.4 - - - +
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Residues in contact with VAL 146 (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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70B ILE* 4.9 2.2 - - + +
109B PHE* 3.7 2.9 - - - +
110B ARG* 2.9 24.5 + - - -
111B ILE* 3.4 45.9 + - + +
112B PRO 5.5 0.4 - - - +
113B VAL* 3.9 20.0 - - + -
119B LEU* 4.0 6.1 - - + -
139B ALA* 2.8 34.8 + - + +
140B GLN 4.1 0.2 - - - +
141B VAL* 3.6 26.5 - - + +
144B LYS* 3.8 8.7 - - + +
145B VAL* 1.3 76.6 - - - +
147B ALA* 1.3 63.7 + - + +
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Residues in contact with ALA 147 (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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70B ILE* 4.2 12.1 - - + -
71B VAL* 6.3 0.4 - - + -
74B MET* 5.1 2.9 - - - -
107B VAL* 6.1 0.2 - - + -
108B LYS 3.2 13.9 - - - +
109B PHE* 4.0 18.2 - - + -
110B ARG* 4.6 1.3 - - - +
138B THR* 3.2 9.5 - - - -
139B ALA* 2.9 40.0 + - + -
145B VAL* 3.4 6.8 - - - +
146B VAL* 1.3 82.9 - - + +
148B GLU* 1.3 65.4 + - - +
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Residues in contact with GLU 148 (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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74B MET* 4.6 1.8 - - - -
106B LYS 3.8 4.3 - - - +
107B VAL* 3.2 4.0 - - - +
108B LYS* 3.1 56.0 + - + +
110B ARG* 2.6 44.2 + - - +
137B GLY 3.3 14.8 - - - +
138B THR* 3.8 11.1 - - + +
145B VAL* 4.4 4.0 - - - +
147B ALA* 1.3 78.6 - - - +
149B ALA* 1.3 64.9 + - - +
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 4.9 10.1 - - + -
74B MET* 4.0 19.5 - - + +
105B ASP 3.8 0.4 - - - -
106B LYS 3.6 9.6 + - - -
107B VAL* 3.6 21.3 - - + -
136B GLY* 3.2 2.8 - - - -
137B GLY 3.0 31.7 + - - -
148B GLU* 1.3 76.7 - - - +
150B GLU* 1.3 64.7 + - - +
151B LEU* 4.0 13.4 - - + +
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Residues in contact with GLU 150 (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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104B ILE* 3.3 4.3 - - - +
105B ASP* 2.7 48.6 + - + +
106B LYS* 3.8 26.1 - - + +
126B LEU* 3.8 29.2 - - + +
135B VAL 3.5 4.5 - - - +
136B GLY* 4.2 3.4 - - - -
137B GLY 5.3 0.4 - - - +
149B ALA* 1.3 77.0 - - - +
151B LEU* 1.3 64.5 + - - +
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Residues in contact with LEU 151 (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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71B VAL* 4.1 11.7 - - + +
74B MET* 4.8 4.7 - - + -
75B ALA* 3.4 41.3 - - + +
101B PHE* 3.5 20.4 - - + -
103B THR* 3.6 7.2 - - - +
104B ILE* 4.3 18.6 - - + +
123B LEU* 4.3 10.8 - - + -
133B TRP 4.0 0.2 - - - +
134B GLN* 3.3 5.2 - - - +
135B VAL* 2.8 48.3 + - + +
149B ALA* 4.0 13.5 - - + +
150B GLU* 1.3 89.3 - - - +
152B LYS* 1.3 61.3 + - - +
153B ALA 4.1 0.7 - - - -
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Residues in contact with LYS 152 (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* 5.7 1.8 - - - +
101B PHE* 3.8 3.1 - - - -
102B MET* 2.9 50.5 + - - +
103B THR* 3.1 44.1 + - - +
132B ILE* 3.9 22.4 - - + -
133B TRP 3.4 5.2 - - - +
134B GLN* 3.5 32.8 - - + +
151B LEU* 1.3 74.0 - - - +
153B ALA* 1.3 62.0 + - - +
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Residues in contact with ALA 153 (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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78B GLY 6.1 0.7 - - - -
79B GLY* 5.5 2.0 - - - +
82B ALA* 5.7 2.0 - - + -
99B VAL* 3.7 24.5 - - + -
100B TYR 3.5 6.7 - - - +
101B PHE* 3.5 26.0 - - + -
102B MET* 4.3 1.0 - - - +
131B MET 4.4 0.2 - - - -
132B ILE* 3.6 8.7 - - - +
133B TRP* 2.8 39.3 + - + +
135B VAL* 6.3 0.4 - - + +
152B LYS* 1.3 76.5 - - - +
154B MET* 1.3 62.4 + - - +
155B ILE* 5.6 1.3 - - + -
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Residues in contact with MET 154 (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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98B ILE 3.4 3.8 - - - +
99B VAL* 3.4 2.1 - - - -
100B TYR* 3.0 63.9 + - + +
102B MET* 3.6 37.0 - - + -
131B MET* 3.4 11.2 - - - +
132B ILE* 4.4 18.4 - - + +
153B ALA* 1.3 75.4 - - - +
155B ILE* 1.3 74.0 + - - +
156B ALA* 4.6 5.4 - - + -
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Residues in contact with ILE 155 (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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82B ALA* 3.9 26.7 - - + -
83B PHE 4.4 0.4 - - - +
86B LEU* 3.7 28.0 - - + -
87B TRP* 3.7 29.8 - - + -
97B LYS* 4.4 12.8 - - + -
98B ILE 3.6 3.6 - - - +
99B VAL* 3.5 28.0 - - + -
131B MET* 2.8 45.7 + - - +
133B TRP* 4.2 10.8 - - + -
153B ALA* 5.6 1.6 - - + -
154B MET* 1.3 77.5 - - - +
156B ALA* 1.3 61.9 - - - +
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Residues in contact with ALA 156 (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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97B LYS* 3.2 12.2 - - - +
98B ILE* 2.8 46.2 + - + +
100B TYR* 4.6 15.7 - - + -
154B MET* 3.7 7.4 + - + -
155B ILE* 1.3 74.7 - - - +
157B GLU* 1.3 63.9 + - - +
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Residues in contact with GLU 157 (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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3001A 2BE 5.6 0.3 + - - -
96B THR* 3.0 25.2 + - - +
97B LYS* 2.7 32.7 + - - +
98B ILE* 4.1 6.4 - - - +
156B ALA* 1.3 77.2 - - - +
158B ARG* 1.3 70.2 + - - +
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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