Contacts of the helix formed by residues 560 - 571 (chain A) in PDB entry 5FWP
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 560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556A SER* 2.8 31.0 + - - +
557A LYS 3.4 2.7 - - - -
559A LYS* 1.3 92.2 - - + +
561A GLU* 1.3 58.4 + - - +
562A ASN 3.4 2.5 - - - -
563A LEU* 3.2 30.0 + - + -
564A CYS* 2.9 33.2 + - - -
580A ILE* 3.8 13.5 - - + -
628A ILE* 5.5 1.3 - - + -
630A PRO* 3.1 46.4 - - + -
635A VAL* 3.4 30.3 - - + -
636A GLU* 3.5 19.7 - - - -
639A ARG* 3.6 18.2 - - + -
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Residues in contact with GLU 561 (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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557A LYS 2.7 17.8 + - - +
558A ALA* 3.1 22.4 + - - +
559A LYS 3.4 0.4 - - - -
560A PHE* 1.3 76.1 - - - +
562A ASN* 1.3 67.0 + - - +
564A CYS* 3.2 8.5 + - - +
565A LYS* 3.0 59.7 + - + +
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Residues in contact with ASN 562 (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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558A ALA 4.7 0.2 + - - -
559A LYS 5.0 2.1 + - - +
560A PHE 3.4 0.2 - - - -
561A GLU* 1.3 82.4 - - - +
563A LEU* 1.3 59.7 + - - +
565A LYS* 3.6 26.6 + - - +
566A LEU* 2.9 29.6 + - - +
642A ALA* 5.6 2.0 - - + -
643A GLU* 6.3 4.5 - - + +
646A LYS* 3.7 35.3 + - - +
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Residues in contact with LEU 563 (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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559A LYS 5.5 0.2 + - - -
560A PHE* 3.2 40.9 + - + +
561A GLU 3.2 0.4 - - - -
562A ASN* 1.3 78.2 - - - +
564A CYS* 1.3 58.3 + - - +
566A LEU* 3.2 9.7 + - + +
567A MET* 2.8 58.6 + - + +
628A ILE* 5.1 2.7 - - + -
635A VAL* 3.5 26.0 - - + +
638A LEU* 3.7 34.3 - - + +
639A ARG* 3.7 12.0 - - + +
642A ALA* 4.2 11.8 - - + +
651A VAL* 6.2 1.1 - - + -
655A VAL* 5.7 2.2 - - + -
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Residues in contact with CYS 564 (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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557A LYS 5.5 0.2 - - - -
560A PHE* 2.9 23.2 + - - -
561A GLU* 3.2 9.6 + - - +
563A LEU* 1.3 74.6 - - - +
565A LYS* 1.3 58.5 + - + +
567A MET 3.4 0.2 + - - -
568A LYS* 2.9 30.4 + - - +
578A VAL* 3.7 25.9 - - - +
579A THR* 4.3 9.2 - - - -
580A ILE* 3.9 23.6 - - - -
628A ILE* 3.4 25.1 - - - -
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Residues in contact with LYS 565 (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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561A GLU* 3.0 45.9 + - - +
562A ASN* 3.6 22.8 + - - +
563A LEU 3.2 0.2 - - - -
564A CYS* 1.3 74.7 - - + +
566A LEU* 1.3 65.2 + - - +
568A LYS* 3.3 9.8 + - - +
569A GLU* 3.1 31.9 + - - +
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Residues in contact with LEU 566 (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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562A ASN 2.9 17.3 + - - +
563A LEU* 3.2 9.2 + - + +
565A LYS* 1.3 76.9 - - - +
567A MET* 1.3 56.6 + - - +
569A GLU* 3.1 22.4 + - + +
570A ILE* 2.8 51.6 + - + +
642A ALA* 3.6 30.1 - - + -
646A LYS* 3.5 45.8 - - + +
651A VAL* 5.3 9.2 - - + -
652A LYS* 4.5 5.6 - - + -
655A VAL* 6.1 0.7 - - + -
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Residues in contact with MET 567 (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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563A LEU* 2.8 42.4 + - + +
564A CYS 3.7 4.0 - - - +
566A LEU* 1.3 76.1 - - + +
568A LYS* 1.3 53.4 + - - +
570A ILE* 3.2 8.7 + - + -
571A LEU* 2.8 40.3 + - + +
578A VAL* 3.9 8.7 - - + -
589A CYS* 5.4 7.0 - - + -
626A LEU* 3.8 26.7 - - + -
628A ILE* 3.5 32.8 - - + -
638A LEU* 5.0 11.4 - - + -
655A VAL* 3.9 31.4 - - + +
658A LEU* 6.0 3.4 - - + -
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Residues in contact with LYS 568 (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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564A CYS 2.9 18.0 + - - +
565A LYS* 3.4 9.9 - - - +
567A MET* 1.3 76.6 - - - +
569A GLU* 1.3 58.4 + - + +
571A LEU* 3.2 4.2 - - - +
572A ASP* 2.9 28.4 + - - +
575A VAL* 5.0 6.5 - - - +
576A GLU 4.3 17.6 + - - -
577A LYS* 4.9 10.1 - - + +
578A VAL* 3.6 28.6 - - + +
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Residues in contact with GLU 569 (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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565A LYS* 3.1 18.8 + - - +
566A LEU* 3.1 23.8 + - + +
568A LYS* 1.3 73.2 - - + +
570A ILE* 1.3 65.6 + - + +
572A ASP* 3.2 22.1 + - - +
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Residues in contact with ILE 570 (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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566A LEU* 2.8 41.4 + - + +
567A MET* 3.4 6.5 - - - +
569A GLU* 1.3 76.4 - - + +
571A LEU* 1.3 61.3 + - + +
572A ASP 3.3 2.6 + - - +
574A LYS* 5.1 2.3 - - - +
651A VAL* 5.1 0.4 - - + -
652A LYS* 3.4 63.5 - - + +
655A VAL* 3.7 28.9 - - + -
656A VAL* 3.6 18.6 - - + +
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Residues in contact with LEU 571 (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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567A MET 2.8 19.0 + - - +
568A LYS 3.2 4.4 - - - +
570A ILE* 1.3 81.4 - - + +
572A ASP* 1.3 58.9 + - - -
573A LYS 3.3 0.5 + - - -
574A LYS* 2.9 32.0 + - + -
575A VAL* 3.1 27.1 + - + +
578A VAL* 4.5 0.7 - - + -
626A LEU* 3.5 31.4 - - + -
655A VAL* 4.1 13.2 - - + -
656A VAL* 4.1 20.4 - - + -
659A PHE* 3.5 46.7 - - + -
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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