Contacts of the helix formed by residues 638 - 649 (chain C) in PDB entry 5Y3R
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 GLN 638 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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631C ARG* 6.3 1.2 - - - +
634C LEU* 2.2 48.8 + - + +
635C PRO* 2.9 19.9 - - - +
636C GLU 2.8 1.1 - - - -
637C LYS* 1.3 84.0 - - - +
639C ALA* 1.3 62.4 + - + +
642C PHE* 2.7 30.2 + - - +
663C ILE* 6.1 2.2 - - - -
667C TYR* 5.7 6.7 - - + -
669C LEU* 5.1 13.2 + - - +
672C ILE* 5.0 17.0 - - - +
673C THR* 6.5 0.9 - - + -
704C PHE* 5.8 1.9 - - - -
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Residues in contact with ALA 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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635C PRO 3.2 9.3 + - - +
636C GLU* 2.8 10.7 + - - +
638C GLN* 1.3 76.0 - - + +
640C GLU* 1.3 71.3 + - + +
642C PHE* 3.0 21.9 - - - +
643C GLU* 3.3 10.8 + - - +
700C LYS* 4.8 21.8 - - + -
703C CYS* 4.8 8.3 - - + +
704C PHE* 5.0 12.6 - - + -
707C PHE* 6.5 0.7 - - - -
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Residues in contact with GLU 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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636C GLU* 3.7 13.5 + - + +
639C ALA* 1.3 81.6 - - + +
641C PHE* 1.3 54.6 + - - +
643C GLU* 2.3 53.0 + - - +
644C PRO* 2.9 12.8 - - + +
700C LYS 5.7 1.7 + - - +
703C CYS* 5.0 6.7 - - - -
1445C ARG* 4.3 18.4 + - - -
1494C GLY 4.7 4.5 - - - +
1495C ASP* 4.4 15.2 - - - +
1498C GLN* 4.2 22.0 - - - +
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Residues in contact with PHE 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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553C VAL* 3.4 14.8 - - + -
554C ASN* 2.9 28.7 - - + -
557C SER* 3.0 36.1 - - - -
636C GLU 3.1 21.2 + - - +
637C LYS* 2.8 48.9 - - + +
640C GLU* 1.3 78.5 - - - +
642C PHE* 1.3 64.2 + - - +
644C PRO* 3.1 14.8 - - + +
645C TRP* 3.4 16.2 - - - -
660C LEU* 5.0 7.9 - - + +
663C ILE* 6.3 2.5 - - + -
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Residues in contact with PHE 642 (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 LYS 3.6 1.3 + - - -
638C GLN 2.7 26.2 + - - +
639C ALA* 3.0 10.5 - - - +
641C PHE* 1.3 76.8 - - - +
643C GLU* 1.3 82.7 + - + +
644C PRO* 3.3 1.2 - - - +
645C TRP* 3.5 9.0 - - - +
646C VAL* 3.1 40.2 - - + +
660C LEU* 3.9 36.5 - - + +
663C ILE* 5.8 0.9 - - + -
664C SER* 4.8 5.8 - - - -
703C CYS* 5.1 1.8 - - + -
707C PHE* 3.6 43.5 - + + -
710C PHE* 3.4 32.3 - + - -
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Residues in contact with GLU 643 (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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639C ALA 3.4 9.2 - - - +
640C GLU* 2.3 40.8 + - - +
642C PHE* 1.3 78.7 - - + +
644C PRO* 1.3 59.9 - - + +
646C VAL* 2.1 46.0 + - + +
647C TYR* 2.9 45.3 + - + -
703C CYS* 2.9 39.0 - - + +
706C LEU* 5.5 2.4 - - + +
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Residues in contact with PRO 644 (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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561C ASN* 5.5 5.6 - - - +
565C TYR* 6.1 0.4 - - - +
640C GLU* 2.9 26.0 - - + +
641C PHE* 3.1 19.1 - - + +
642C PHE 3.3 1.8 - - - +
643C GLU* 1.3 79.2 - - + +
645C TRP* 1.3 63.6 + - + +
647C TYR* 3.2 18.5 - - + +
648C SER* 2.8 36.0 + - - -
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Residues in contact with TRP 645 (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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557C SER* 2.8 53.8 - - - -
558C GLU* 4.3 0.2 - - - -
560C LEU* 4.0 6.1 - - + -
561C ASN* 3.0 42.6 + - - +
564C LEU* 3.5 22.2 - - + -
616C LYS* 3.3 14.8 - - - -
641C PHE* 3.4 32.4 + + - -
642C PHE 3.5 5.4 - - - +
643C GLU 2.7 2.0 + - - -
644C PRO* 1.3 80.7 - - + +
646C VAL* 1.3 56.8 + - - +
648C SER* 2.4 36.8 + - - -
649C PHE* 2.9 10.0 + - - -
656C GLN* 4.0 14.6 + - - +
660C LEU* 4.4 18.6 - - + -
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Residues in contact with VAL 646 (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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642C PHE* 3.1 50.3 - - + +
643C GLU* 2.1 36.5 + - + +
645C TRP* 1.3 67.9 - - - +
647C TYR* 1.3 69.2 + - + +
649C PHE* 3.2 20.9 + - - +
656C GLN* 5.6 0.7 - - - +
660C LEU* 3.6 14.1 - - + -
710C PHE* 3.4 38.3 - - + -
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Residues in contact with TYR 647 (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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643C GLU* 2.9 62.1 + - + -
644C PRO* 3.2 18.8 - - + +
646C VAL* 1.3 84.3 - - + +
648C SER* 1.3 54.3 + - - +
649C PHE* 2.7 12.6 + - - +
650C SER* 3.8 12.3 + - - -
706C LEU* 4.3 15.5 - - + +
1384C PHE* 6.2 0.3 - - - -
1388C ASP* 3.1 38.3 + - + -
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Residues in contact with SER 648 (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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561C ASN* 4.5 1.9 + - - -
564C LEU* 5.2 7.4 - - - -
565C TYR* 2.9 31.3 + - - -
644C PRO 2.8 19.8 + - - -
645C TRP* 2.4 28.0 + - - -
647C TYR* 1.3 68.9 - - - +
649C PHE* 1.3 63.3 + - - -
650C SER 2.8 3.0 + - - -
651C TYR* 2.8 30.2 - - - -
653C LEU* 5.7 0.5 - - - +
656C GLN* 4.1 6.4 + - - -
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Residues in contact with PHE 649 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645C TRP 2.9 3.8 + - - +
646C VAL* 3.2 18.8 - - - +
647C TYR 2.7 4.2 + - - +
648C SER* 1.3 77.6 - - - +
650C SER* 1.3 64.3 + - - +
651C TYR* 2.3 20.3 + - - +
652C GLU* 2.6 39.8 + - - -
653C LEU* 4.1 2.6 + - - +
656C GLN* 3.2 43.4 + - + +
710C PHE* 6.3 0.4 - - + -
714C VAL* 6.4 2.0 - - + -
717C LYS* 3.0 45.8 - - + -
718C MET* 6.2 2.7 - - + -
722C LYS* 5.6 0.9 - - + -
730C LEU* 5.9 5.8 - - + -
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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