Contacts of the strand formed by residues 555 - 564 (chain B) in PDB entry 4P3N
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 TYR 555 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493B SER* 4.9 3.2 + - - -
494B PHE 5.2 1.2 - - - -
495B LYS* 3.6 47.9 - - + +
547B GLN* 3.9 29.2 + - + +
548B ILE 3.2 15.5 - - - -
549B LYS* 3.6 35.2 - - + +
553B GLY 4.1 9.2 - - - -
554B ARG* 1.3 73.5 - - - +
556B HIS* 1.3 68.6 + - - +
557B GLN 4.3 0.4 - - - -
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Residues in contact with HIS 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B GLN* 4.1 3.1 - - - -
548B ILE* 2.9 53.6 + - + +
550B ASP* 2.9 31.7 + - - +
554B ARG* 3.8 18.0 + - + -
555B TYR* 1.3 77.9 + - - +
557B GLN* 1.3 63.2 + - - +
558B CYS* 3.2 3.8 + - - +
599B ARG* 3.8 13.6 + - - +
603B ILE* 3.7 49.1 - - + +
606B GLU* 5.8 4.3 - - - -
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Residues in contact with GLN 557 (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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497B ASN* 4.9 1.0 - - - +
545B ASP* 3.4 29.5 + - - +
546B ILE 2.9 23.6 + - - +
547B GLN* 3.8 25.4 - - + +
556B HIS* 1.3 70.5 - - - +
558B CYS* 1.3 58.0 + - - +
559B ALA 2.8 29.3 + - - -
560B THR* 4.9 1.0 - - - -
599B ARG* 2.6 32.5 + - - +
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Residues in contact with CYS 558 (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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487B TYR* 3.9 12.8 - - - +
546B ILE 3.1 9.1 + - - +
548B ILE* 4.5 13.7 - - + -
556B HIS* 3.2 8.9 + - - +
557B GLN* 1.3 75.3 + - - +
559B ALA* 1.3 66.7 + - - +
560B THR* 3.8 3.8 + - - +
592B ALA* 4.4 2.9 - - - +
593B ILE 4.0 5.8 - - - +
594B LEU 3.8 22.2 - - - -
595B GLY* 4.0 18.0 + - - -
599B ARG* 4.0 19.1 - - - +
600B MET* 4.7 11.0 - - - -
603B ILE* 4.3 14.8 - - - -
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Residues in contact with ALA 559 (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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483B LEU* 3.4 25.1 - - + -
487B TYR* 3.1 20.6 + - - +
546B ILE* 3.2 28.8 + - + -
557B GLN* 2.8 24.1 + - - -
558B CYS* 1.3 79.2 - - - +
560B THR* 1.3 61.5 + - - +
592B ALA 3.2 12.3 - - - +
593B ILE 3.9 1.6 - - - +
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Residues in contact with THR 560 (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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543B LYS* 4.8 4.9 - - - +
544B ILE 3.3 8.8 + - - -
545B ASP* 3.0 21.0 + - - -
546B ILE* 4.1 1.1 - - - -
557B GLN* 4.9 0.7 - - - -
558B CYS 3.8 3.1 + - - +
559B ALA* 1.3 78.1 - - - +
561B ILE* 1.3 73.0 + - - +
562B GLN* 4.5 10.0 + - + +
590B HIS* 4.9 6.5 - - + +
591B ARG* 3.4 21.5 - - - +
592B ALA* 3.2 17.4 + - + +
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Residues in contact with ILE 561 (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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476B ILE* 3.7 22.4 - - + -
479B CYS* 3.9 33.0 - - + +
480B LEU* 4.0 26.2 - - + -
483B LEU* 4.6 2.9 - - + -
519B LEU* 5.9 0.4 - - + -
543B LYS* 3.3 4.3 - - - +
544B ILE* 2.8 59.0 + - + +
546B ILE* 4.1 10.3 - - + -
559B ALA* 6.1 0.2 - - + -
560B THR* 1.3 79.4 + - - +
562B GLN* 1.3 59.5 + - - +
563B LEU* 4.2 3.2 + - + +
589B VAL* 3.7 24.2 - - + -
590B HIS 3.6 2.0 - - - +
591B ARG* 4.7 4.0 - - + -
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Residues in contact with GLN 562 (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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538B ALA* 4.2 3.9 - - - +
540B TYR* 3.2 32.6 + - + +
541B GLY 3.2 20.2 + - - -
542B PRO 3.5 1.7 + - - -
543B LYS* 3.5 26.0 - - + +
560B THR* 4.6 11.6 + - + +
561B ILE* 1.3 75.7 - - - +
563B LEU* 1.3 89.0 + - - +
589B VAL* 3.4 1.9 - - - -
590B HIS* 2.9 64.7 + - + +
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Residues in contact with LEU 563 (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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472B ILE* 3.6 36.6 - - + -
476B ILE* 4.3 15.5 - - + -
515B ALA* 3.8 19.5 - - + -
519B LEU* 4.6 10.5 - - + -
540B TYR* 3.6 0.7 - - - +
541B GLY* 3.2 11.5 - - - -
542B PRO* 3.1 33.1 + - + +
561B ILE* 5.1 1.8 - - + -
562B GLN* 1.3 103.0 + - - +
564B ASP* 1.3 59.3 + - - +
565B PHE* 4.3 6.7 - - + -
587B VAL* 4.2 4.5 - - + -
588B ILE 3.4 3.1 - - - +
589B VAL* 3.6 30.7 - - + -
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Residues in contact with ASP 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B TYR* 3.6 19.6 - - - +
563B LEU* 1.3 73.7 - - - +
565B PHE* 1.3 62.1 + - - +
566B GLN* 2.8 29.3 + - - +
567B LEU* 2.8 31.8 + - - +
568B PRO* 3.5 7.5 - - - +
587B VAL* 4.0 0.9 - - - +
588B ILE* 2.8 39.7 + - + +
590B HIS* 3.0 33.7 + - + +
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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