Contacts of the strand formed by residues 352 - 357 (chain A) in PDB entry 3NKO
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 ASN 352 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A PRO* 3.6 24.4 + - - +
164A PRO 2.8 12.4 + - - +
165A LEU* 3.4 16.9 - - + +
166A ILE 2.8 26.5 + - - -
351A VAL* 1.3 75.8 - - - +
353A VAL* 1.3 60.2 + - - +
490A TYR 3.5 2.5 - - - +
491A GLY* 3.4 3.8 - - - -
492A PRO* 3.2 11.2 - - - +
493A THR* 2.8 50.5 + - - +
494A PHE* 4.1 11.5 - - + -
515A LEU* 4.0 14.1 + - + +
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Residues in contact with VAL 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ILE* 3.4 11.9 - - + +
168A PHE* 4.7 11.0 - - + -
191A LEU* 4.6 19.7 - - + -
338A LEU* 5.1 9.9 - - + -
339A MET* 4.3 25.4 - - + -
342A LEU* 4.6 6.7 - - + -
351A VAL* 4.0 17.5 - - + +
352A ASN* 1.3 77.4 - - - +
354A ILE* 1.3 74.3 + - - +
355A PHE* 4.1 1.7 + - + +
488A VAL* 3.7 0.9 - - - +
489A GLY* 3.5 3.8 - - - -
490A TYR* 2.8 47.1 + - + +
494A PHE* 4.1 0.6 - - - -
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Residues in contact with ILE 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 3.9 21.3 - - + -
166A ILE 2.9 10.5 + - - +
167A ILE* 4.5 9.0 - - + -
168A PHE* 2.7 35.7 + - - +
353A VAL* 1.3 77.3 - - - +
355A PHE* 1.3 58.8 + - - +
356A VAL* 3.9 23.1 - - + -
487A PHE* 3.7 26.0 - - + -
488A VAL 3.4 2.5 - - - -
494A PHE* 3.8 19.5 - - + -
508A LEU* 4.9 8.5 - - + -
511A VAL* 5.5 0.2 - - + -
512A MET* 4.0 24.7 - - + -
515A LEU* 3.9 17.0 - - + -
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Residues in contact with PHE 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A PHE* 3.4 41.7 - + + -
170A VAL* 3.9 19.1 - - + -
173A PHE* 4.0 14.8 - + - -
188A ILE* 3.7 39.7 - - + -
191A LEU* 4.6 17.0 - - + -
331A ILE* 4.5 0.2 - - + -
335A VAL* 3.9 16.6 - - + -
353A VAL* 4.1 2.1 - - + +
354A ILE* 1.3 72.5 - - - +
356A VAL* 1.3 61.3 + - - +
486A VAL* 4.0 30.0 - - + +
487A PHE* 3.4 3.5 - - - -
488A VAL* 2.9 48.0 + - + +
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Residues in contact with VAL 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 4.1 10.1 - - + -
168A PHE 3.0 8.2 + - - +
169A SER* 3.2 19.6 - - - +
170A VAL* 3.0 22.0 + - - -
201A MET* 3.3 37.9 - - + -
216A LEU* 4.2 14.4 - - + -
354A ILE* 3.9 18.6 - - + -
355A PHE* 1.3 78.8 - - - +
357A GLY* 1.3 60.8 + - - +
486A VAL* 3.4 10.5 - - - +
487A PHE* 4.5 2.2 - - + -
508A LEU* 4.0 13.9 - - + -
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Residues in contact with GLY 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A SER* 6.1 0.7 - - - -
170A VAL* 3.2 14.1 - - - -
173A PHE* 4.6 0.9 - - - -
201A MET* 3.4 13.0 - - - +
213A LEU* 5.9 0.2 - - - -
216A LEU* 4.0 6.9 - - - +
356A VAL* 1.3 77.4 - - - +
358A ASP* 1.3 60.9 + - - -
485A THR* 3.1 28.5 - - - +
486A VAL* 3.2 19.3 + - - +
505A ASN* 5.7 0.3 + - - -
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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