Contacts of the helix formed by residues 630 - 641 (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 SER 630 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547C TYR* 4.1 8.4 - - - -
629C TRP* 1.3 77.3 - - - +
631C TYR* 1.3 70.2 + - - -
633C GLY* 2.8 17.5 + - - -
634C TYR 3.1 9.2 + - - -
653C VAL 2.9 14.5 + - - -
654C ALA 3.3 15.5 - - - -
655C PRO* 3.5 7.7 - - - +
656C VAL 3.8 1.6 + - - -
740C HIS* 3.1 18.5 + - - -
801C 8VU 2.9 41.1 - - - -
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Residues in contact with TYR 631 (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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547C TYR* 3.1 33.8 - - + +
548C ALA 3.3 16.1 + - - -
549C GLY* 3.5 7.0 - - - -
550C PRO* 3.7 20.7 - - + +
594C ILE* 5.7 0.7 - - - +
598C LEU* 3.3 20.9 - - + +
599C GLY 4.3 0.2 + - - -
602C GLU* 2.9 25.0 + - - +
629C TRP 3.1 0.2 + - - -
630C SER* 1.3 82.7 + - - +
632C GLY* 1.3 57.4 + - - +
634C TYR* 3.1 11.3 + + + +
635C VAL* 3.0 39.7 + - + +
656C VAL* 5.4 0.2 - - - -
659C TRP* 3.4 28.4 - + - -
666C TYR* 3.6 8.3 - - - -
801C 8VU 3.1 30.6 - - - -
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Residues in contact with GLY 632 (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* 3.3 25.9 - - - +
547C TYR* 3.5 15.7 + - - -
628C GLY* 3.3 7.6 - - - -
629C TRP 2.9 11.1 + - - -
631C TYR* 1.3 79.0 - - - +
633C GLY* 1.3 55.8 - - - +
635C VAL* 3.9 1.1 - - - -
636C THR* 2.8 32.4 + - - -
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Residues in contact with GLY 633 (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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628C GLY 3.3 21.8 - - - -
629C TRP 3.4 0.8 - - - +
630C SER 2.8 10.2 + - - -
632C GLY* 1.3 77.1 - - - +
634C TYR* 1.3 58.8 + - - +
636C THR* 3.7 4.1 - - - -
637C SER* 2.8 34.1 + - - -
652C ALA* 3.9 5.0 - - - +
653C VAL 4.5 0.7 - - - -
655C PRO* 3.2 16.9 - - - +
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Residues in contact with TYR 634 (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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599C GLY* 3.4 28.1 - - - -
602C GLU* 4.5 2.7 - - - -
603C VAL* 4.9 0.9 - - + -
630C SER 3.1 6.9 + - - +
631C TYR* 3.4 15.0 - + + +
633C GLY* 1.3 73.9 - - - +
635C VAL* 1.3 71.1 + - + +
637C SER* 3.2 3.6 + - - -
638C MET* 2.9 52.8 + - + +
655C PRO* 3.5 1.2 - - - +
656C VAL* 3.0 50.5 - - + +
657C SER 4.6 2.9 - - - -
659C TRP* 3.3 35.6 + + + -
686C SER* 2.7 44.7 + - - -
688C VAL* 4.1 7.2 - - + -
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Residues in contact with VAL 635 (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* 3.6 26.0 - - + -
547C TYR 3.7 8.3 - - - +
548C ALA* 4.0 6.3 - - + -
602C GLU* 4.2 9.9 - - + +
603C VAL* 4.3 11.9 - - + -
606C GLN* 4.0 17.9 - - + -
626C ILE* 5.2 0.2 - - + -
631C TYR* 3.0 38.5 + - + +
632C GLY 4.1 0.9 - - - +
634C TYR* 1.3 79.3 - - + +
636C THR* 1.3 58.1 + - - +
638C MET* 3.2 5.5 + - - +
639C VAL* 2.8 39.7 + - + +
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Residues in contact with THR 636 (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* 3.2 8.2 - - - +
626C ILE* 3.7 28.0 - - + +
627C TRP* 3.2 6.2 - - - -
628C GLY 3.1 13.5 + - - -
632C GLY 2.8 25.0 + - - -
633C GLY* 3.7 5.2 - - - -
635C VAL* 1.3 77.3 - - - +
637C SER* 1.3 57.7 + - - +
639C VAL* 3.7 1.7 - - - +
640C LEU* 3.0 41.6 + - + +
651C ILE 3.2 28.7 - - - +
652C ALA* 4.4 3.1 - - + -
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Residues in contact with SER 637 (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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633C GLY 2.8 21.9 + - - -
634C TYR* 3.7 4.5 - - - -
636C THR* 1.3 76.8 - - - +
638C MET* 1.3 62.2 + - - +
640C LEU* 3.5 2.0 + - - -
641C GLY* 3.1 18.2 + - - -
652C ALA* 3.5 5.2 - - - +
655C PRO* 4.3 5.1 - - - +
688C VAL* 4.1 27.3 - - - +
691C ARG* 5.4 0.5 - - - +
695C PHE* 3.2 17.1 - - - -
700C TYR* 2.8 29.4 + - - -
719C ILE* 4.6 1.1 - - - +
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Residues in contact with MET 638 (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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599C GLY 4.0 9.4 - - - +
603C VAL* 3.9 18.2 - - + -
634C TYR* 2.9 43.7 + - + +
635C VAL 3.8 3.1 - - - +
637C SER* 1.3 75.7 - - - +
639C VAL* 1.3 58.4 + - - +
641C GLY 3.6 0.7 + - - -
642C SER* 3.1 15.1 + - - -
686C SER* 3.7 28.3 - - - +
687C THR 3.6 16.6 - - - +
688C VAL* 3.7 21.3 - - + -
691C ARG* 2.9 58.8 + - - +
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Residues in contact with VAL 639 (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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603C VAL* 3.7 30.1 - - + +
606C GLN* 4.4 4.9 - - + -
607C ILE* 3.9 9.6 - - + -
626C ILE* 3.8 22.4 - - + -
635C VAL* 2.8 26.8 + - + +
636C THR 3.7 3.1 - - - +
638C MET* 1.3 75.6 - - - +
640C LEU* 1.3 64.6 + - - +
642C SER* 2.5 27.8 + - - -
643C GLY 4.4 0.2 + - - -
644C SER* 4.6 2.4 + - - -
647C PHE* 3.4 40.1 - - + -
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Residues in contact with LEU 640 (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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626C ILE* 4.0 12.1 - - + -
636C THR* 3.0 23.7 + - + +
637C SER 4.1 0.2 - - - +
639C VAL* 1.3 75.7 - - - +
641C GLY* 1.3 56.6 + - - +
642C SER 3.3 0.7 + - - -
643C GLY* 4.4 3.3 + - - -
647C PHE* 4.1 10.1 - - + -
649C CYS 3.7 24.0 - - - +
650C GLY* 3.5 22.7 - - - +
694C ASN 3.6 14.6 - - - +
695C PHE* 3.8 15.9 - - + -
697C GLN* 5.5 0.2 - - - +
698C VAL* 3.8 37.5 - - + +
699C GLU 4.7 1.3 - - - +
700C TYR* 3.5 33.9 - - + -
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Residues in contact with GLY 641 (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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637C SER 3.1 12.4 + - - -
638C MET 3.6 4.5 - - - -
639C VAL 3.1 0.4 - - - -
640C LEU* 1.3 75.5 - - - +
642C SER* 1.3 55.9 + - - +
643C GLY 3.3 2.7 - - - -
691C ARG* 3.4 25.2 - - - +
694C ASN* 3.2 26.0 + - - +
695C PHE* 3.7 23.3 - - - -
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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