Contacts of the strand formed by residues 96 - 102 (chain B) in PDB entry 1DXO
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 LEU 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B ARG 3.2 2.0 + - - -
5B ALA* 3.2 3.5 - - + +
6B LEU 2.9 25.1 + - - -
29B LEU* 4.0 26.7 - - + -
34B TRP* 3.6 22.9 - - + -
94B ALA* 3.8 1.2 - - - +
95B ASP* 1.3 79.1 - - - +
97B VAL* 1.3 66.5 + - - +
98B ILE* 4.2 17.5 - - + -
141B LYS* 3.3 25.4 - - + +
143B VAL* 3.6 25.6 - - + -
184B LEU* 4.3 7.6 - - + -
211B LEU* 4.8 1.8 - - + -
214B ILE* 4.0 25.4 - - + -
215B TRP* 4.3 4.7 - - + -
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Residues in contact with VAL 97 (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 LEU* 3.3 16.8 - - + +
8B VAL* 4.7 2.5 - - + -
91B LEU* 4.1 24.0 - - + -
94B ALA* 3.7 22.2 - - + +
95B ASP 5.3 0.4 - - - -
96B LEU* 1.3 80.9 - - - +
98B ILE* 1.3 64.6 + - - +
99B PHE* 3.5 35.0 - - + -
140B LYS* 5.3 1.3 - - + -
141B LYS 2.9 12.6 + - - +
142B ALA* 3.2 4.0 - - - +
143B VAL* 2.9 26.7 + - - +
181B PHE* 4.1 20.0 - - + -
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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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5B ALA* 5.8 0.4 - - + -
6B LEU 2.8 14.5 + - - +
7B ILE* 3.4 22.6 - - + -
8B VAL* 2.6 35.9 + - - +
25B ALA* 4.4 13.5 - - + -
29B LEU* 4.5 6.5 - - + -
96B LEU* 4.2 21.8 - - + -
97B VAL* 1.3 75.4 - - - +
99B PHE* 1.3 68.7 + - - +
100B GLN* 3.9 4.0 + - + +
143B VAL* 3.5 13.9 - - + +
145B SER* 4.5 5.6 - - - -
207B TRP* 4.1 23.6 - - + -
211B LEU* 3.9 28.0 - - + -
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Residues in contact with PHE 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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8B VAL* 3.4 22.0 - - + -
91B LEU* 5.7 0.2 - - + -
97B VAL* 3.5 27.8 - - + -
98B ILE* 1.3 73.5 - - - +
100B GLN* 1.3 57.1 - - - +
101B PHE* 3.6 13.2 - - + -
112B LEU* 4.2 10.1 - - + -
115B TRP* 3.5 29.8 - + - -
116B PHE* 3.5 29.2 - + - -
120B PHE* 4.9 3.8 - + - -
142B ALA* 4.2 7.6 - - + -
143B VAL 2.9 16.7 + - - +
144B LEU* 3.6 28.6 - - + -
145B SER 2.8 31.2 + - - +
176B LEU* 3.9 22.4 - - + -
181B PHE* 5.5 1.8 - + - -
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Residues in contact with GLN 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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7B ILE* 4.6 12.3 - - + -
8B VAL 3.0 10.3 + - - +
9B LEU* 3.4 18.0 - - + +
10B ALA 3.0 24.8 + - - -
18B ASN* 2.9 43.0 + - - +
21B MET* 3.1 32.3 - - + +
22B LYS* 4.5 4.0 - - + +
98B ILE* 3.8 3.6 - - + +
99B PHE* 1.3 71.0 - - - +
101B PHE* 1.3 65.4 + - - +
145B SER* 2.9 43.4 + - - -
147B THR* 4.2 6.7 - - - +
207B TRP* 4.4 2.8 + - - -
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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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8B VAL 5.7 0.2 - - - -
10B ALA* 3.9 18.6 - - + -
18B ASN* 2.9 12.1 + - - +
99B PHE* 3.6 19.7 - - + -
100B GLN* 1.3 76.1 - - - +
102B PRO* 1.3 82.2 - - + +
103B LEU* 4.4 2.0 - - + -
107B GLY 4.1 5.6 - - - -
108B VAL* 3.5 31.9 - - + -
109B PRO* 3.6 12.3 - - + -
112B LEU* 3.8 13.9 - - + -
144B LEU* 3.9 22.9 - - + -
145B SER 3.1 5.5 + - - +
146B ILE* 3.2 64.4 - - + -
147B THR 3.3 1.7 + - - -
171B ILE* 5.2 2.2 - - + -
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Residues in contact with PRO 102 (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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10B ALA 3.3 20.0 - - - +
11B HIS* 4.1 11.0 - - + +
18B ASN* 3.5 15.0 - - - +
101B PHE* 1.3 98.2 - - + +
103B LEU* 1.3 63.9 + - - +
104B GLN* 3.4 27.2 + - - +
109B PRO* 3.8 4.2 - - + +
147B THR* 3.4 12.1 - - - +
301B FAD 3.3 31.9 - - - +
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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