Contacts of the helix formed by residues 601 - 614 (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 SER 601 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599C ASN 3.5 3.1 + - - -
600C SER* 1.3 87.2 + - - +
602C LEU* 1.3 62.6 + - - +
603C ALA* 3.1 9.2 + - - +
604C GLU* 3.0 41.9 + - - +
605C PHE* 3.3 12.5 + - - +
644C GLY 3.5 9.2 + - - -
645C ASN* 4.5 13.8 + - - -
646C LYS 3.5 8.7 - - - -
648C MET* 4.1 1.8 - - - +
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Residues in contact with LEU 602 (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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601C SER* 1.3 73.0 - - - +
603C ALA* 1.3 58.4 + - - +
605C PHE* 3.2 4.6 + - + +
606C VAL* 2.9 37.3 + - + +
622C LEU* 4.2 17.0 - - + -
638C LEU* 4.0 30.1 - - + -
639C ASP 4.1 10.3 - - - +
640C ASN* 4.1 12.8 - - - +
643C ASP 3.7 21.5 - - - +
644C GLY* 3.2 20.7 + - - +
646C LYS 3.1 7.5 + - - -
648C MET* 4.0 21.5 - - + -
651C LEU* 3.8 18.2 - - + -
658C TRP* 5.5 2.2 - - + -
660C ILE* 6.0 0.4 - - + -
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Residues in contact with ALA 603 (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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601C SER* 3.1 7.4 + - - +
602C LEU* 1.3 77.0 - - - +
604C GLU* 1.3 58.3 + - + +
606C VAL* 3.1 9.3 + - - +
607C GLN* 2.9 29.5 + - - +
617C GLN* 4.9 2.6 - - - +
640C ASN* 5.4 2.7 - - - +
644C GLY* 2.9 18.8 + - - +
645C ASN* 5.4 5.2 - - - +
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Residues in contact with GLU 604 (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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600C SER* 3.7 18.7 + - - +
601C SER* 3.0 36.7 + - - +
603C ALA* 1.3 77.7 - - + +
605C PHE* 1.3 58.4 + - - +
607C GLN* 3.4 9.4 + - - +
608C SER* 2.9 29.3 + - - -
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Residues in contact with PHE 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567C VAL* 3.5 25.1 - - + -
569C ILE* 4.1 6.3 - - + -
594C PHE* 3.8 34.8 - + + -
596C VAL* 3.9 19.5 - - + -
600C SER* 4.3 6.9 + - - +
601C SER 3.3 10.1 + - - +
602C LEU* 3.2 8.6 + - + +
604C GLU* 1.3 77.4 - - - +
606C VAL* 1.3 62.3 + - - +
608C SER* 4.3 6.7 - - - -
609C LEU* 2.9 58.9 + - + +
622C LEU* 4.3 20.9 - - + -
648C MET* 3.6 27.1 - - + -
660C ILE* 4.6 2.2 - - + -
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Residues in contact with VAL 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602C LEU* 2.9 24.5 + - + +
603C ALA* 3.1 9.8 + - - +
605C PHE* 1.3 76.3 - - - +
607C GLN* 1.3 60.0 + - - +
609C LEU* 3.9 4.7 - - - +
610C SER* 2.9 28.9 + - - -
617C GLN* 4.2 26.7 - - + +
620C ILE* 4.3 13.5 - - + +
622C LEU* 4.1 22.7 - - + -
640C ASN* 3.8 35.9 - - - +
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Residues in contact with GLN 607 (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 ALA 2.9 12.5 + - - +
604C GLU* 3.6 12.8 - - - +
606C VAL* 1.3 77.1 - - - +
608C SER* 1.3 76.0 + - - +
610C SER* 3.1 4.3 + - - +
611C GLN* 2.9 38.7 + - - +
617C GLN* 3.4 28.2 - - - +
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Residues in contact with SER 608 (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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594C PHE* 4.8 10.0 - - - -
604C GLU 2.9 17.9 + - - -
605C PHE* 3.8 10.7 - - - -
607C GLN* 1.3 85.4 + - - +
609C LEU* 1.3 54.9 + - - +
611C GLN* 3.9 3.0 - - - +
612C THR* 2.6 43.1 + - - -
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Residues in contact with LEU 609 (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* 3.7 23.6 - - + -
594C PHE* 4.3 14.1 - - + -
605C PHE* 2.9 50.7 + - + +
606C VAL* 3.9 4.5 - - - +
608C SER* 1.3 73.6 - - - +
610C SER* 1.3 63.2 + - - +
613C MET* 2.9 55.6 + - + +
615C PHE* 5.2 2.5 - - + -
620C ILE* 3.9 19.1 - - + -
622C LEU* 4.6 12.1 - - + -
662C LEU* 4.1 13.0 - - + -
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Residues in contact with SER 610 (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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606C VAL 2.9 16.5 + - - -
607C GLN* 3.1 8.7 + - - +
609C LEU* 1.3 80.6 - - - +
611C GLN* 1.3 62.1 + - - +
614C GLY* 3.0 8.7 + - - -
615C PHE* 2.8 51.3 + - - +
617C GLN* 3.4 31.5 + - - +
620C ILE* 4.4 7.0 - - - -
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Residues in contact with GLN 611 (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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607C GLN* 2.9 30.0 + - - +
608C SER* 3.9 4.3 - - - +
610C SER* 1.3 83.2 + - - +
612C THR* 1.3 67.3 + - - +
614C GLY* 3.7 6.9 + - - -
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Residues in contact with THR 612 (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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594C PHE* 4.4 23.7 - - + -
608C SER* 2.6 29.9 + - - -
609C LEU 3.9 2.5 - - - -
611C GLN* 1.3 83.6 - - - +
613C MET* 1.3 60.9 + - + +
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Residues in contact with MET 613 (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* 4.3 8.5 - - + -
571C ALA* 6.1 4.0 - - + -
592C THR* 3.8 35.0 - - + +
594C PHE* 4.3 12.8 - - + -
609C LEU* 2.9 40.5 + - + +
612C THR* 1.3 80.3 - - + +
614C GLY* 1.3 63.7 + - - +
615C PHE* 3.6 24.6 - - + -
662C LEU* 3.9 18.6 - - + -
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Residues in contact with GLY 614 (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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610C SER 3.0 7.3 + - - -
611C GLN 3.7 6.2 + - - -
612C THR 3.4 3.6 - - - -
613C MET* 1.3 80.0 - - - +
615C PHE* 1.3 74.1 + - - +
616C PRO* 4.8 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