Contacts of the strand formed by residues 87 - 90 (chain M) in PDB entry 6CNB
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 VAL 87 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85M LEU* 4.6 1.8 - - + -
86M HIS* 1.3 83.1 - - - +
88M PHE* 1.3 63.5 + - - +
173M ILE* 3.8 16.2 - - + -
175M ARG 4.0 2.8 + - - -
176M VAL* 3.5 43.3 - - + +
177M ALA 3.7 7.5 + - - +
306N VAL* 5.9 3.8 - - + -
394N VAL* 3.3 28.9 - - + -
395N ILE 2.9 23.8 - - - +
396N ALA* 4.0 4.9 - - + +
397N LEU* 4.2 4.8 - - - +
412N VAL* 4.6 5.4 - - + -
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Residues in contact with PHE 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86M HIS* 6.2 0.2 - - + -
87M VAL* 1.3 77.7 - - - +
89M GLN* 1.3 64.1 + - - +
90M TYR* 4.8 6.3 - + + -
119M TRP* 3.1 43.1 - + + -
121M ILE* 3.5 35.2 - - + -
177M ALA* 3.8 23.1 - - + +
178M GLN 5.2 2.9 - - - -
179M LEU* 4.4 17.0 - - + -
394N VAL* 3.0 8.6 - - - +
395N ILE* 2.8 51.4 + - + -
397N LEU* 3.4 27.5 - - + +
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Residues in contact with GLN 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543B LEU* 2.8 33.4 + - - +
544B ILE 3.6 7.7 + - - -
88M PHE* 1.3 73.7 - - - +
90M TYR* 1.3 62.2 + - - +
176M VAL* 5.6 6.1 - - + -
177M ALA 3.6 5.1 + - - +
178M GLN* 2.9 38.6 + - - +
179M LEU* 3.2 20.4 + - - +
389N THR* 4.0 4.7 + - - -
392N GLN* 3.4 21.3 - - + +
393N ASP 4.0 5.8 - - - -
394N VAL* 3.4 33.1 - - + +
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Residues in contact with TYR 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88M PHE* 4.8 7.6 - + + -
89M GLN* 1.3 78.6 - - - +
91M ALA* 1.3 63.1 + - - +
92M ASN* 3.6 21.1 - - + +
93M ARG* 3.6 47.9 + - + +
103M GLU 5.4 0.9 + - - -
105M PRO* 3.9 27.0 - - + +
148M LEU* 4.9 3.8 - - + -
178M GLN* 5.0 0.2 - - - -
179M LEU* 3.6 40.2 - - + +
391N LEU 4.3 1.6 - - - +
392N GLN* 3.2 24.8 - - - +
393N ASP* 3.1 34.2 + - + +
395N ILE* 4.7 12.8 - - + -
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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