Contacts of the strand formed by residues 579 - 584 (chain B) in PDB entry 2FJN
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 ARG 579 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573B LYS* 4.0 1.0 - - - +
574B MET* 2.9 32.2 + - - +
577B ALA* 3.3 5.8 - - + +
578B GLN* 1.3 80.8 + - - +
580B SER* 1.3 71.8 + - - +
581B TYR* 3.5 26.7 - - + +
699B ARG* 3.6 13.9 - - - +
704B LEU* 3.5 52.9 + - - +
705B SER* 5.5 0.4 - - - +
706B PRO* 5.8 2.2 - - - +
729B ASP* 2.9 37.6 + - - -
733B LEU* 3.4 38.9 - - + +
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Residues in contact with SER 580 (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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571B LEU* 4.2 9.3 - - - +
572B ILE 3.2 5.6 - - - -
573B LYS* 3.5 32.7 - - - +
579B ARG* 1.3 81.7 - - - +
581B TYR* 1.3 68.7 + - - +
710B PRO* 3.6 28.0 - - - +
711B VAL* 4.2 4.5 + - - +
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Residues in contact with TYR 581 (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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570B SER 3.6 0.5 - - - +
571B LEU* 3.5 2.9 - - - +
572B ILE* 2.7 55.7 + - + +
574B MET* 4.1 9.9 - - + -
579B ARG* 3.5 23.3 + - + +
580B SER* 1.3 74.6 - - - +
582B ILE* 1.3 62.9 + - - +
583B LEU* 3.5 18.2 - - + -
704B LEU* 5.0 3.1 - - + -
710B PRO* 4.2 2.0 - - - -
711B VAL* 3.7 27.1 - - + +
713B VAL* 4.4 2.9 - - + -
725B PHE* 5.0 3.8 - + - -
726B CYS* 3.6 31.4 - - + -
729B ASP* 2.5 36.8 + - + -
730B THR* 2.7 32.5 + - - -
753B MET* 5.2 0.4 - - + -
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Residues in contact with ILE 582 (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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557B ILE* 3.8 23.3 - - + -
569B ALA* 4.1 5.2 - - + -
570B SER 3.2 9.0 - - - +
571B LEU* 4.2 2.7 - - + -
581B TYR* 1.3 74.1 - - - +
583B LEU* 1.3 60.9 + - - +
598B MET* 3.7 31.0 - - + -
602B GLN* 3.7 32.1 - - + +
710B PRO* 3.5 29.8 - - + +
711B VAL 2.9 11.9 + - - +
712B VAL* 4.2 15.0 - - + +
713B VAL* 2.7 33.4 + - - +
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Residues in contact with LEU 583 (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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569B ALA* 3.2 1.6 - - - -
570B SER 2.7 36.0 + - - -
572B ILE* 4.0 20.4 - - + -
581B TYR* 3.5 28.7 - - + -
582B ILE* 1.3 74.6 - - - +
584B THR* 1.3 60.6 + - - +
713B VAL* 3.3 5.2 - - + +
718B GLY 3.9 16.4 - - - +
722B SER* 4.0 29.2 - - - +
723B GLY* 4.2 1.3 - - - +
726B CYS* 3.7 14.8 - - + -
753B MET* 4.6 1.1 - - + -
757B ARG* 3.7 20.0 + - - -
760B LEU* 4.0 27.4 - - + -
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Residues in contact with THR 584 (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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567B ILE* 4.3 7.1 - - - +
568B ASN 2.5 24.1 + - - -
569B ALA* 3.6 13.2 - - - +
583B LEU* 1.3 76.3 - - - +
585B GLN* 1.3 70.9 + - - +
595B PHE* 3.7 24.2 - - + -
598B MET* 4.1 6.0 - - + +
712B VAL* 3.8 9.6 - - + -
713B VAL 3.0 8.9 + - - +
714B HIS* 3.1 34.3 - - + +
718B GLY* 3.1 18.3 + - - -
757B ARG* 4.2 2.9 - - - +
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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