Contacts of the strand formed by residues 567 - 574 (chain B) in PDB entry 4N41
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 ALA 567 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539B SER 3.4 12.7 + - - +
540B ARG* 3.4 31.8 - - + +
541B VAL* 2.9 24.8 + - - +
565B GLY 3.6 4.3 + - - +
566B ILE* 1.3 78.4 - - - +
568B TYR* 1.3 65.0 + - - +
625B ASP* 5.8 2.0 - - - +
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Residues in contact with TYR 568 (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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540B ARG* 4.3 5.4 + - - +
541B VAL* 3.1 23.8 - - + +
543B LEU* 4.0 8.7 - - + -
558B LEU* 3.4 59.8 + - + +
559B GLU* 5.6 1.0 + - - -
561B LEU* 3.8 14.4 - - + -
562B ALA* 4.4 11.3 - - + +
566B ILE 3.7 15.7 - - - -
567B ALA* 1.3 77.7 - - - +
569B ASP* 1.3 78.2 + - - +
623B ALA* 4.2 14.1 - - + -
624B GLY* 3.3 20.7 - - - -
625B ASP* 5.3 0.5 - - - +
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Residues in contact with ASP 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B ALA* 5.9 1.2 - - - +
540B ARG* 3.5 11.8 + - - -
541B VAL 3.1 7.6 + - - +
542B LEU* 3.9 20.5 - - + +
543B LEU* 2.6 37.9 + - - +
568B TYR* 1.3 79.7 - - - +
570B LEU* 1.3 58.4 + - - +
571B VAL* 4.9 0.2 - - + -
621B HIS* 2.8 29.0 + - + +
623B ALA 3.2 4.9 - - - +
624B GLY* 3.1 13.2 - - - -
626B THR* 2.6 36.8 + - - -
631B LEU* 3.9 5.8 - - + +
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Residues in contact with LEU 570 (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 LEU* 3.5 17.3 - - + +
545B ARG* 3.5 30.7 - - + -
551B GLN* 4.6 10.8 - - + +
554B PHE* 3.7 38.8 - - + -
558B LEU* 4.2 22.2 - - + -
568B TYR* 4.9 0.2 - - - -
569B ASP* 1.3 72.9 - - - +
571B VAL* 1.3 68.4 + - - +
572B SER 4.2 0.4 - - - -
621B HIS* 3.7 1.6 - - - -
622B GLU* 2.8 47.2 + - + +
623B ALA* 2.9 26.2 + - + +
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Residues in contact with VAL 571 (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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542B LEU* 4.1 18.2 - - + -
543B LEU 2.9 10.2 + - - +
544B LEU* 3.6 12.6 - - + -
545B ARG* 3.3 26.7 + - - +
569B ASP* 4.9 0.2 - - + -
570B LEU* 1.3 80.6 - - - +
572B SER* 1.3 69.3 + - - +
573B VAL* 3.8 3.8 + - + +
601B PHE* 5.1 2.9 - - + -
619B LEU* 3.7 34.3 - - + -
620B VAL 3.3 9.0 - - - +
621B HIS* 4.3 4.5 - - + +
631B LEU* 4.0 27.4 - - + -
635B ILE* 4.1 8.5 - - + -
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Residues in contact with SER 572 (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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545B ARG* 3.7 26.6 + - - -
546B ASP 3.0 19.6 + - - -
547B GLY* 3.6 6.9 - - - -
570B LEU 4.2 0.4 - - - -
571B VAL* 1.3 73.1 - - - +
573B VAL* 1.3 58.7 + - - +
574B ARG* 3.6 24.5 + - - -
618B LYS 3.6 1.2 - - - +
619B LEU* 3.2 7.1 - - - -
620B VAL* 2.9 35.0 + - - -
622B GLU* 3.8 12.2 + - - -
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Residues in contact with VAL 573 (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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544B LEU* 4.4 9.6 - - + -
545B ARG 2.9 12.7 + - - +
546B ASP* 3.5 19.7 - - - +
571B VAL* 4.1 13.2 - - + +
572B SER* 1.3 77.3 + - - +
574B ARG* 1.3 63.6 + - - +
575B LYS* 3.9 3.1 + - - +
617B LEU* 4.0 34.1 - - + -
618B LYS 3.8 2.0 - - - -
619B LEU* 3.9 22.4 - - + -
635B ILE* 5.1 0.2 - - + -
652B LEU* 4.1 16.1 - - + +
653B PRO* 4.6 7.6 - - + -
656B LEU* 3.8 20.0 - - + +
5F C 3.6 3.1 + - - -
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Residues in contact with ARG 574 (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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545B ARG* 5.3 1.4 - - - +
547B GLY* 3.7 31.3 + - - -
572B SER* 3.6 25.2 + - - -
573B VAL* 1.3 72.8 - - - +
575B LYS* 1.3 63.8 + - - +
576B SER 3.4 16.9 + - - +
617B LEU* 3.6 7.2 - - - -
618B LYS* 2.9 57.4 + - + +
620B VAL* 4.0 25.0 - - - +
622B GLU* 4.6 6.7 + - - -
3F A 4.3 2.0 + - - -
4F C 3.1 44.2 + - - +
5F C 3.5 4.5 - - - -
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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