Contacts of the strand formed by residues 487 - 493 (chain A) in PDB entry 4N2F
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 PHE 487 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A ILE* 4.0 17.5 - - + -
415A PRO* 3.7 32.8 - - + -
416A PRO 3.8 13.0 - - - -
417A VAL* 3.8 22.2 - - + -
478A PHE* 3.7 30.7 - + - -
479A VAL 3.3 15.0 - - - +
481A ILE* 4.1 5.7 - - - +
485A LYS 5.3 2.0 - - - -
486A LYS* 1.3 81.8 + - - +
488A LEU* 1.3 78.1 + - - +
489A LEU 4.7 0.9 - - - -
559A LEU* 5.9 0.4 - - + -
561A LEU* 3.9 23.6 - - + -
565A ASP* 4.4 13.2 - - + +
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Residues in contact with LEU 488 (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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478A PHE* 3.3 7.8 - - - -
479A VAL* 2.8 48.6 + - + +
481A ILE* 3.8 25.4 - - + -
487A PHE* 1.3 86.2 - - - +
489A LEU* 1.3 64.3 + - - +
490A LEU* 3.9 4.4 + - + -
564A GLN 3.9 8.3 - - - +
565A ASP* 3.4 27.8 - - - +
566A ILE* 4.3 1.8 - - - +
567A ILE* 3.8 17.7 - - + +
622A LEU* 5.6 0.2 - - + -
625A LEU* 3.6 31.6 - - + -
627A LEU* 5.3 1.8 - - + -
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Residues in contact with LEU 489 (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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476A MET* 4.1 22.0 - - + -
477A SER 3.6 13.9 - - - +
478A PHE* 3.8 23.8 - - + -
487A PHE* 4.4 2.2 - - - -
488A LEU* 1.3 72.4 - - - +
490A LEU* 1.3 68.6 + - - +
491A MET* 3.9 26.9 - - + -
552A ARG* 5.4 2.0 - - + -
555A LEU* 4.1 18.2 - - + -
556A LYS* 5.8 0.2 - - + -
561A LEU* 4.2 19.7 - - + -
565A ASP 2.8 12.6 + - - +
566A ILE* 3.3 23.4 - - + +
567A ILE 3.0 24.8 + - - -
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Residues in contact with LEU 490 (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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476A MET* 3.2 8.8 - - - +
477A SER* 2.8 54.0 + - - +
479A VAL* 3.8 37.2 - - + -
488A LEU* 4.5 4.7 - - + -
489A LEU* 1.3 79.2 - - - +
491A MET* 1.3 61.2 + - - +
567A ILE* 3.4 28.5 - - + +
569A LEU* 4.2 12.1 - - + -
589A VAL* 3.6 7.2 - - + +
591A MET* 3.7 25.8 - - + -
622A LEU* 4.4 15.5 - - + -
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Residues in contact with MET 491 (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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475A PHE* 3.5 22.9 - - + +
476A MET* 4.1 13.2 - - - -
489A LEU* 3.9 18.4 - - + -
490A LEU* 1.3 75.2 - - - +
492A ALA* 1.3 63.4 + - - +
548A LEU* 3.5 37.0 - - + +
552A ARG* 4.1 22.4 - - + +
555A LEU* 3.9 24.0 - - - -
566A ILE* 3.9 11.4 - - + -
567A ILE 3.0 7.3 + - - +
568A ASP* 3.3 18.5 - - - +
569A LEU* 2.8 25.7 + - - -
589A VAL* 4.8 2.5 - - - -
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Residues in contact with ALA 492 (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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474A GLU 4.5 5.4 - - - +
475A PHE* 3.0 27.7 + - + +
491A MET* 1.3 78.7 - - - +
493A SER* 1.3 59.0 + - - +
545A GLN* 4.6 1.2 + - - -
548A LEU* 3.4 34.8 - - + +
568A ASP* 4.4 0.9 - - - +
569A LEU* 3.6 7.4 - - - -
571A ALA* 3.7 19.3 - - + -
573A PHE* 4.6 4.9 - - + -
587A ASN* 5.7 0.2 - - - +
589A VAL* 4.5 10.4 - - + +
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Residues in contact with SER 493 (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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492A ALA* 1.3 75.3 - - - +
494A THR* 1.3 62.7 + - - +
495A SER* 3.5 3.8 + - - -
496A ALA* 3.0 23.0 + - - +
497A CYS 3.6 2.9 + - - -
545A GLN* 3.2 17.1 + - - -
548A LEU* 4.2 0.2 - - - -
568A ASP* 3.7 29.2 + - - +
569A LEU 2.8 14.4 + - - -
570A PRO* 3.4 6.2 - - - +
571A ALA* 3.0 21.6 + - - +
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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