Contacts of the strand formed by residues 619 - 629 (chain C) in PDB entry 5Y7K
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 VAL 619 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528C MET* 5.4 0.4 - - + -
539C LYS* 4.1 13.3 + - - +
540C TYR 3.5 3.6 - - - +
542C LEU* 3.8 43.5 - - + -
574C ILE* 4.7 4.5 - - + -
613C PHE* 3.2 29.4 - - + +
614C SER* 3.4 22.3 - - - +
616C MET* 4.7 2.2 - - + -
617C GLY 3.5 3.6 + - - +
618C PHE* 1.3 102.6 - - + +
620C ASP* 1.3 67.5 + - - +
621C ASN 3.1 7.6 + - - -
624C ILE* 4.2 5.6 - - + -
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Residues in contact with ASP 620 (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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539C LYS* 4.0 25.6 + - + +
540C TYR 2.9 21.3 + - - +
619C VAL* 1.3 70.4 - - - +
621C ASN* 1.3 57.2 + - - +
622C LYS* 3.0 41.9 + - - +
623C ARG* 2.8 63.4 + - + +
624C ILE* 3.8 4.2 - - - +
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Residues in contact with ASN 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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340B LEU* 4.0 30.7 - - + +
343B ARG* 5.8 0.2 - - - +
539C LYS* 4.9 9.3 + - - +
614C SER* 3.7 32.5 + - - +
615C LYS* 5.5 4.9 - - - +
619C VAL 3.1 5.3 + - - -
620C ASP* 1.3 69.8 - - - +
622C LYS* 1.3 81.3 + - - +
623C ARG 3.4 0.9 - - - -
624C ILE* 4.2 17.9 + - - +
646C VAL 4.5 7.8 - - - +
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Residues in contact with LYS 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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338B ASN* 6.6 0.9 - - + -
340B LEU* 4.1 18.4 - - + +
539C LYS* 5.2 5.9 - - - +
620C ASP* 3.0 25.2 + - - +
621C ASN* 1.3 93.0 + - - +
623C ARG* 1.3 65.2 + - + +
624C ILE 4.0 1.1 - - - -
648C LYS* 3.6 20.9 - - - +
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Residues in contact with ARG 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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539C LYS* 4.4 8.9 + - - +
541C PRO* 3.3 41.0 - - + +
542C LEU 3.1 22.2 + - - -
620C ASP* 2.8 35.0 + - - +
622C LYS* 1.3 87.0 - - + +
624C ILE* 1.3 61.7 + - - +
648C LYS* 4.7 6.5 - - + -
762C CYS 4.7 3.4 - - - +
763C PHE* 3.0 56.7 + - + +
764C SER* 5.0 3.9 + - - -
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Residues in contact with ILE 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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542C LEU* 3.2 22.7 - - + +
610C ALA* 4.3 11.0 - - + +
613C PHE 5.3 0.2 - - - -
614C SER* 3.5 36.8 - - - -
619C VAL* 4.2 11.7 - - + -
620C ASP 3.8 9.4 - - - +
621C ASN* 4.2 10.9 + - - +
622C LYS 4.0 0.6 - - - -
623C ARG* 1.3 79.7 - - - +
625C ALA* 1.3 64.0 + - - +
646C VAL* 3.8 20.6 + - + +
647C PHE* 3.3 32.4 - - + -
648C LYS* 2.8 33.2 + - - +
763C PHE* 4.2 1.5 - - - -
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Residues in contact with ALA 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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542C LEU 2.8 7.2 + - - +
543C LEU* 3.3 16.4 - - + -
544C LEU* 2.7 30.1 + - - +
624C ILE* 1.3 75.3 - - - +
626C ILE* 1.3 57.5 + - - +
647C PHE* 3.8 4.5 - - - -
649C CYS* 3.4 33.7 - - - +
650C GLY 5.0 0.2 - - - +
759C ILE* 4.2 7.4 - - + -
763C PHE* 3.7 18.5 - - + -
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Residues in contact with ILE 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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543C LEU* 3.9 2.5 - - - -
544C LEU* 3.5 34.3 - - + +
546C VAL* 3.8 11.0 - - + -
606C GLN* 5.3 0.2 - - + -
625C ALA* 1.3 78.8 - - - +
627C TRP* 1.3 63.4 + - - +
635C VAL* 5.0 0.7 - - + -
636C THR* 3.7 22.1 - - + +
639C VAL* 3.8 33.0 - - + -
640C LEU* 4.0 21.8 - - + -
647C PHE* 3.6 21.1 - - + -
649C CYS 3.4 9.9 + - - +
650C GLY* 2.9 26.9 - - - -
651C ILE* 3.0 2.4 + - - +
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Residues in contact with TRP 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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543C LEU* 3.6 33.7 - - + +
544C LEU 3.1 19.8 + - - +
545C ASP* 3.7 30.7 + - - +
546C VAL* 3.2 14.6 + - - +
563C TRP* 3.6 31.7 - + + -
575C VAL* 5.4 1.0 - - - +
626C ILE* 1.3 76.0 - - - +
628C GLY* 1.3 78.1 + - - +
629C TRP* 4.2 17.7 - + + -
636C THR* 3.2 6.3 - - - -
651C ILE* 3.1 27.4 - - + +
653C VAL* 4.2 13.0 - - + -
752C TYR* 4.0 20.9 - + - -
755C MET* 4.1 26.2 - - + -
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Residues in contact with GLY 628 (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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545C ASP* 5.4 0.7 - - - -
546C VAL 3.5 8.3 - - - -
627C TRP* 1.3 87.1 - - - +
629C TRP* 1.3 58.9 + - - +
632C GLY 3.3 17.3 - - - -
633C GLY* 3.3 11.9 - - - -
636C THR* 3.1 4.8 + - - -
651C ILE 3.2 3.1 + - - +
652C ALA* 3.8 0.7 - - - -
653C VAL* 3.1 26.9 + - - +
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Residues in contact with TRP 629 (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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546C VAL 4.3 1.8 + - - -
547C TYR* 3.6 10.1 - - + -
627C TRP* 4.2 20.6 - + + -
628C GLY* 1.3 73.6 - - - -
630C SER* 1.3 97.2 + - - +
631C TYR 3.1 0.2 + - - -
632C GLY* 2.9 15.7 + - - -
633C GLY 3.4 2.1 - - - +
653C VAL* 3.4 34.3 - - + +
654C ALA* 4.1 4.9 - - - +
740C HIS* 2.9 29.7 + + - -
741C GLY* 3.2 29.8 - - - -
742C ILE* 3.6 21.8 - - + -
748C HIS* 6.1 0.4 - - - -
751C ILE* 4.2 11.4 - - + -
752C TYR* 4.0 27.8 - + - -
755C MET* 5.2 0.2 - - + -
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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