Contacts of the helix formed by residues 663 - 672 (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 ASP 663 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201C TRP* 3.8 14.0 - - + -
202C VAL* 3.8 8.0 - - + +
206C GLU* 2.5 35.6 - - - +
256C TYR* 3.0 25.9 + - + +
257C PRO* 3.1 13.0 - - + +
662C TYR* 1.3 98.9 + - - +
664C SER* 1.3 63.6 + - - +
665C VAL 3.3 2.9 + - - -
666C TYR 3.0 21.0 + - - -
667C THR* 2.8 25.5 + - - -
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Residues in contact with SER 664 (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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202C VAL* 4.8 0.2 - - - +
257C PRO* 2.8 17.4 + - - +
258C LYS 3.7 9.6 - - - -
259C ALA* 4.1 7.0 - - - +
263C ASN* 2.5 34.5 + - - -
318C ARG* 4.0 1.3 - - - -
663C ASP* 1.3 72.1 - - - +
665C VAL* 1.3 68.1 + - - +
668C GLU* 2.7 63.6 + - - +
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Residues in contact with VAL 665 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C VAL* 3.4 26.5 - - + -
203C TYR* 6.0 0.2 - - + -
206C GLU* 3.6 18.8 - - + -
207C VAL* 4.1 16.4 - - + -
263C ASN* 5.0 0.2 - - - +
299C TYR* 3.6 36.6 - - + +
320C GLN* 2.6 36.2 + - - +
663C ASP* 3.3 1.0 + - - -
664C SER* 1.3 78.7 + - - +
666C TYR* 1.3 61.0 + - - +
669C ARG* 3.2 26.6 + - - +
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Residues in contact with TYR 666 (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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206C GLU* 3.4 33.6 - - - +
357C PHE* 4.6 7.7 - + - -
547C TYR* 4.9 1.4 + - - -
549C GLY* 4.5 1.6 - - - -
550C PRO* 3.2 25.3 + - - +
598C LEU* 5.2 0.7 - - + -
631C TYR* 3.6 4.5 - + - -
659C TRP* 4.1 14.1 - + - -
662C TYR* 3.5 21.1 - + + -
663C ASP* 3.0 9.2 + - - +
665C VAL* 1.3 77.2 - - - +
667C THR* 1.3 69.6 + - - +
669C ARG* 3.4 17.2 + - - +
670C TYR* 3.0 53.8 - + - -
801C 8VU 3.5 53.5 - + + -
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Residues in contact with THR 667 (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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259C ALA* 4.2 5.4 - - + -
598C LEU* 5.6 1.1 - - - -
659C TRP* 3.6 44.3 + - + +
662C TYR* 3.5 23.9 - - - +
663C ASP 2.8 20.9 + - - -
664C SER 4.2 0.4 - - - -
666C TYR* 1.3 80.2 - - - +
668C GLU* 1.3 60.0 + - - +
670C TYR* 2.9 7.1 + - - +
671C MET* 2.8 30.5 + - + +
683C TYR* 3.4 19.7 - - + +
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Residues in contact with GLU 668 (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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259C ALA* 4.6 1.8 - - - -
260C GLY* 2.8 20.3 + - - +
299C TYR* 3.8 4.7 + - - -
318C ARG* 2.7 67.1 + - - +
319C ILE* 5.7 1.2 - - - -
320C GLN* 4.4 6.4 + - - +
664C SER* 2.7 32.1 + - - +
667C THR* 1.3 71.0 - - - +
669C ARG* 1.3 59.1 + - - +
670C TYR 3.2 0.2 - - - -
672C GLY* 2.9 47.6 + - - +
673C LEU* 4.4 10.1 - - + +
683C TYR* 4.2 4.5 - - - +
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Residues in contact with ARG 669 (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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206C GLU* 3.4 26.3 + - - +
320C GLN* 2.9 31.3 + - + +
353C TRP* 3.6 48.2 - - + +
354C VAL 5.9 0.4 - - - -
357C PHE* 3.0 42.8 + - - +
595C ASN* 4.2 4.0 + - - -
665C VAL* 3.2 38.4 + - - +
666C TYR* 3.4 16.5 + - - +
667C THR 3.1 1.2 + - - -
668C GLU* 1.3 79.4 - - - +
670C TYR* 1.3 90.6 + - + +
801C 8VU 5.7 0.6 - - - +
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Residues in contact with TYR 670 (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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353C TRP* 3.5 50.9 - + + -
356C ARG 4.4 1.9 + - - -
357C PHE* 3.6 18.2 - - - -
550C PRO* 3.5 24.5 + - + +
594C ILE* 4.9 0.7 - - + -
595C ASN* 4.0 7.4 - - - +
596C ARG* 2.6 33.9 + - - -
598C LEU* 3.5 27.8 - - + +
666C TYR* 3.0 59.0 - + - -
667C THR 2.9 3.1 + - - +
669C ARG* 1.3 107.6 + - - +
671C MET* 1.3 59.2 + - - +
672C GLY 3.8 0.7 - - - -
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Residues in contact with MET 671 (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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596C ARG* 3.6 15.3 - - - +
597C ARG 3.8 0.2 - - - -
598C LEU* 3.3 50.3 - - + +
659C TRP* 4.7 6.3 - - + -
667C THR* 2.8 18.9 + - + +
670C TYR* 1.3 81.7 - - - +
672C GLY* 1.3 62.9 + - - +
679C ASN* 2.8 41.3 + - - +
682C HIS* 3.7 36.1 - - + +
683C TYR* 3.2 28.6 - - + +
686C SER* 4.3 7.2 - - - +
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Residues in contact with GLY 672 (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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319C ILE* 6.2 5.2 - - - -
596C ARG* 4.6 7.7 - - - +
668C GLU* 2.9 29.0 + - - +
670C TYR 3.8 0.6 - - - -
671C MET* 1.3 77.5 - - - +
673C LEU* 1.4 64.0 + - - -
678C ASP* 3.5 9.9 - - - -
683C TYR* 2.7 26.2 + - - -
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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