Contacts of the strand formed by residues 78 - 83 (chain B) in PDB entry 3RLQ
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 ILE 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B ILE* 4.0 28.0 - - + +
52B SER* 3.8 22.4 - - - -
53B SER 4.2 2.5 - - - +
56B LEU* 3.6 20.0 - - + -
77B HIS* 1.3 77.1 - - - +
79B ASN* 1.3 70.1 + - - +
80B LEU* 4.3 9.2 - - + -
91B ILE* 4.1 21.3 - - + -
92B VAL 3.2 9.6 - - - +
93B ASP* 4.3 1.1 - - + -
214B ILE* 4.2 15.9 - - + -
216B TYR* 4.7 2.5 - - + -
217B PRO 2.9 13.3 + - - +
218B ILE* 3.2 15.2 - - + -
219B THR 2.8 24.8 + - - -
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Residues in contact with ASN 79 (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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178A GLU* 4.7 4.0 + - - -
77B HIS* 3.9 28.9 + - - -
78B ILE* 1.3 80.8 - - - +
80B LEU* 1.3 65.1 + - - +
81B ILE* 4.6 9.1 - - + +
90B THR 3.7 0.7 - - - +
91B ILE* 3.4 4.3 - - - +
92B VAL* 2.8 53.3 + - + +
219B THR* 3.2 10.9 + - - -
221B PHE* 3.4 35.8 - - + -
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU* 4.2 4.7 - - + -
45B LEU* 4.4 11.7 - - + -
49B ILE* 4.3 7.4 - - + -
78B ILE* 4.3 7.6 - - + -
79B ASN* 1.3 80.6 - - - +
81B ILE* 1.3 62.7 + - - +
82B PRO* 3.8 1.8 - - - -
89B LEU* 4.9 7.9 - - + -
90B THR 3.4 2.5 - - - +
91B ILE* 3.7 31.4 - - + -
203B ILE* 3.8 26.5 - - + -
207B VAL* 3.9 13.5 - - + -
218B ILE* 3.8 26.7 - - + -
219B THR 2.8 11.6 + - - +
220B LEU* 3.4 13.3 - - + +
221B PHE 2.9 25.5 + - - -
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Residues in contact with ILE 81 (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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221A PHE* 4.1 16.2 - - + -
79B ASN* 4.6 7.0 - - + +
80B LEU* 1.3 83.3 - - - +
82B PRO* 1.3 60.8 - - - +
83B ASN* 3.6 3.0 + - + +
88B THR 3.7 0.9 - - - +
89B LEU* 3.7 3.4 - - - +
90B THR* 2.8 46.3 + - + +
92B VAL* 4.4 18.8 - - + -
185B LYS* 6.3 0.2 - - + -
221B PHE* 3.4 31.0 - - + +
223B GLU* 3.7 25.8 - - + +
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Residues in contact with PRO 82 (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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80B LEU 3.8 0.4 - - - -
81B ILE* 1.3 84.2 - - - +
83B ASN* 1.3 59.5 + - - +
84B LYS* 4.0 1.6 - - + +
88B THR 3.6 6.1 - - - +
89B LEU* 3.7 6.7 - - + -
198B LEU* 3.4 37.5 - - + +
200B GLU 5.7 0.4 - - - +
203B ILE* 3.8 19.7 - - + -
220B LEU* 3.4 21.5 - - + -
221B PHE 3.2 14.1 - - - +
222B VAL* 4.1 15.8 - - + +
223B GLU* 3.1 28.5 + - - +
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Residues in contact with ASN 83 (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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81B ILE* 3.6 2.7 + - + +
82B PRO* 1.3 73.6 - - - +
84B LYS* 1.3 58.1 + - - +
85B GLN* 3.1 21.3 + - - +
86B ASP* 3.1 29.2 + - - -
87B ARG* 2.8 23.9 + - - -
88B THR* 2.7 31.3 + - - +
198B LEU* 4.4 1.1 - - - -
223B GLU* 3.1 44.4 + - - +
225B GLU* 3.4 10.3 + - - +
231B HIS* 5.4 0.2 - - - -
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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