Contacts of the strand formed by residues 620 - 627 (chain C) in PDB entry 4YOC
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 ILE 620 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606C VAL* 4.3 22.2 - - + +
609C LEU* 3.9 25.1 - - + -
610C SER* 4.4 15.0 - - - -
615C PHE* 3.6 34.5 - - + -
616C PRO 4.2 2.5 - - - +
617C GLN 3.7 18.2 - - - +
618C ASP 4.7 0.7 - - - -
619C GLN* 1.3 85.4 + - - +
621C ARG* 1.3 60.2 + - - +
622C LEU* 4.5 9.0 - - + -
640C ASN* 4.3 9.3 + - - +
662C LEU* 3.8 15.0 - - + -
663C GLU 3.5 3.6 - - - -
664C THR* 3.9 13.2 - - + -
676C LEU* 3.7 8.3 - - - +
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Residues in contact with ARG 621 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620C ILE* 1.3 75.4 - - - +
622C LEU* 1.3 75.2 + - - +
623C TRP* 3.3 30.6 - - + +
638C LEU 5.0 9.4 - - - +
640C ASN* 5.3 5.4 - - + +
661C PHE 3.7 0.7 - - - +
662C LEU* 3.8 0.3 - - - +
663C GLU* 2.9 41.2 + - - +
676C LEU* 3.7 22.7 - - + +
677C PRO 2.4 31.9 + - - -
678C LYS* 4.8 8.9 - - - +
679C PHE* 4.0 20.8 - - - +
706C TYR* 3.0 32.5 + - - -
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Residues in contact with LEU 622 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569C ILE* 5.4 0.2 - - + -
602C LEU* 4.2 17.5 - - + -
605C PHE* 4.3 19.1 - - + -
606C VAL* 4.1 25.1 - - + -
609C LEU* 4.6 8.3 - - + -
620C ILE* 4.5 13.7 - - + -
621C ARG* 1.3 84.4 - - - +
623C TRP* 1.3 64.8 + - - +
624C PRO* 3.7 1.3 - - - -
638C LEU* 3.4 41.9 + - + +
640C ASN* 5.1 11.1 - - + +
660C ILE* 3.7 22.0 - - + -
661C PHE 3.7 1.8 - - - +
662C LEU* 3.7 21.8 - - + -
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Residues in contact with TRP 623 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621C ARG* 3.3 24.4 - - + +
622C LEU* 1.3 77.9 - - - +
624C PRO* 1.3 67.4 - - - +
625C MET 3.3 0.2 + - - -
635C PRO* 4.0 9.8 - - + +
636C ALA* 3.2 27.8 - - - +
637C MET* 3.9 19.3 - - + -
638C LEU 4.9 0.4 - - - -
660C ILE* 3.9 0.2 - - - -
661C PHE* 2.9 52.0 + + + +
663C GLU* 2.7 37.8 + - + +
679C PHE* 3.6 33.9 - + - -
686C MET* 3.4 30.9 - - + -
706C TYR* 3.4 21.1 - + - -
762C ASP* 4.0 17.9 - - + -
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Residues in contact with PRO 624 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622C LEU 3.5 10.5 - - - +
623C TRP* 1.3 83.5 - - - +
625C MET* 1.3 63.8 + - - +
626C GLN* 3.2 6.0 + - + +
636C ALA* 2.8 46.4 + - + +
637C MET 4.9 2.0 - - - +
638C LEU* 3.5 28.9 - - + +
658C TRP* 3.8 35.4 - - + +
659C THR 3.8 5.2 - - - +
660C ILE* 3.9 9.4 - - + -
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Residues in contact with MET 625 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570C VAL* 3.8 16.8 - - + -
575C PHE* 4.6 3.1 - - + -
583C MET* 4.7 2.5 - - - -
584C TYR* 3.3 29.4 - - + +
623C TRP 3.3 2.4 + - - -
624C PRO* 1.3 69.1 - - - +
626C GLN* 1.3 59.4 + - - +
633C LYS* 3.5 35.7 - - + +
634C ARG* 3.8 4.0 - - - -
635C PRO* 3.6 31.2 - - + -
655C GLU* 4.6 8.5 - - - +
658C TRP* 4.7 7.3 + - - -
659C THR* 2.7 34.9 + - - +
661C PHE* 3.5 38.8 - - + +
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Residues in contact with GLN 626 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624C PRO* 3.2 5.5 + - + +
625C MET* 1.3 74.5 - - - +
627C ALA* 1.3 70.9 + - - +
628C ARG* 3.9 5.8 + - + +
633C LYS* 3.4 4.0 - - - -
634C ARG* 2.9 34.4 + - - +
636C ALA* 3.7 32.2 - - + +
655C GLU* 5.8 2.7 - - - +
761C MET* 5.4 9.9 - - - +
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Residues in contact with ALA 627 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625C MET 4.3 0.6 + - - -
626C GLN* 1.3 85.5 + - - +
628C ARG* 1.3 65.2 + - - +
631C GLY* 5.9 1.1 - - - +
632C THR 3.4 10.1 - - - +
633C LYS* 4.1 13.9 - - + +
655C GLU* 5.8 4.7 + - - +
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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