Contacts of the strand formed by residues 498 - 504 (chain A) in PDB entry 3NGN
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 MET 498 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A PHE* 4.1 17.5 - - - -
354A LEU* 4.5 2.2 - - + -
404A PRO* 3.7 17.9 - - + -
405A LEU 3.6 18.4 - - - +
406A VAL* 4.1 15.7 - - + -
493A TYR* 3.5 26.6 - - + -
494A SER* 3.2 38.5 + - - +
495A LYS* 3.4 15.8 + - - +
496A THR 3.7 0.6 - - - -
497A HIS* 1.3 85.2 - - + +
499A ASN* 1.3 71.6 + - - +
536A LEU* 4.4 6.3 - - + -
537A GLU 3.0 14.1 - - - +
538A LEU* 3.8 15.9 - - + -
539A HIS* 5.0 1.1 - - - -
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Residues in contact with ASN 499 (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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178A LYS* 3.1 31.7 - - + +
493A TYR* 4.3 5.2 - - - -
495A LYS 5.2 1.0 - - - +
498A MET* 1.3 79.0 - - - +
500A VAL* 1.3 61.3 + - - +
501A LEU 3.6 0.2 + - - -
536A LEU* 3.3 10.9 - - - +
537A GLU* 2.9 59.1 + - + +
539A HIS* 3.6 19.3 + - - -
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Residues in contact with VAL 500 (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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177A LEU* 3.9 16.5 - - + +
178A LYS* 3.4 19.2 + - - +
468A SER 5.3 0.2 - - - +
469A ALA* 4.1 22.4 - - + +
493A TYR* 3.0 30.9 + - + +
499A ASN* 1.3 72.8 - - - +
501A LEU* 1.3 63.7 + - - +
502A GLY 3.8 7.6 - - - +
503A VAL* 4.1 3.8 - - + -
534A THR* 3.0 28.9 - - - +
535A GLN 3.6 5.8 - - - +
536A LEU* 3.9 6.7 - - + -
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Residues in contact with LEU 501 (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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174A TRP* 5.1 1.3 - - - -
176A THR* 3.6 3.5 - - - -
177A LEU 2.6 31.0 + - - -
178A LYS* 3.0 38.0 + - + +
179A GLU 4.2 5.2 - - - +
180A ARG* 3.8 27.4 - - + +
188A SER* 4.0 8.1 - - - -
499A ASN* 4.7 0.4 - - + +
500A VAL* 1.3 76.8 - - - +
502A GLY* 1.3 52.8 + - - +
535A GLN* 2.9 49.7 + - + +
536A LEU 4.4 0.4 - - - -
537A GLU* 3.8 37.7 - - + +
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Residues in contact with GLY 502 (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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174A TRP* 3.5 17.5 - - - -
175A ILE 3.1 13.7 - - - -
177A LEU* 4.2 6.3 - - - -
500A VAL* 3.6 1.5 - - - -
501A LEU* 1.3 81.3 - - - +
503A VAL* 1.3 64.7 + - - -
534A THR* 3.0 8.7 + - - -
535A GLN* 2.9 27.1 + - - +
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Residues in contact with VAL 503 (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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174A TRP* 3.7 7.5 - - - -
175A ILE* 2.9 44.3 + - + +
177A LEU* 4.4 3.4 - - + -
469A ALA 3.5 24.7 - - - +
470A TYR* 3.6 35.7 - - + -
474A LEU* 3.6 27.1 - - + -
500A VAL* 4.1 3.1 - - + -
502A GLY* 1.3 80.6 - - - +
504A LEU* 1.3 63.1 + - - +
505A GLY* 3.3 1.3 + - - +
533A LEU 3.4 4.7 - - - -
534A THR* 3.7 12.1 - - - +
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Residues in contact with LEU 504 (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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172A ARG* 3.1 68.8 + - + +
173A PRO 3.8 8.5 - - - +
174A TRP* 3.5 18.1 - - + +
227A GLU* 5.7 0.2 - - - +
231A CYS* 4.6 11.9 - - - -
470A TYR* 2.6 25.4 + - - +
503A VAL* 1.3 69.4 - - - +
505A GLY* 1.3 61.0 + - - +
531A SER* 5.0 0.4 - - - +
533A LEU* 2.9 43.3 + - + +
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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