Contacts of the helix formed by residues 663 - 672 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201D TRP* 3.5 7.2 - - + -
202D VAL* 3.8 14.4 - - + -
206D GLU* 2.8 32.8 - - - +
256D TYR* 3.2 25.1 + - + +
257D PRO 3.2 11.2 - - - +
662D TYR* 1.3 97.3 - - - +
664D SER* 1.3 61.5 + - - +
665D VAL* 3.4 2.3 - - - +
666D TYR* 3.0 32.4 + - - +
667D THR* 2.7 33.1 + - - -
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Residues in contact with SER 664 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D PRO* 2.8 17.7 + - - +
258D LYS 3.6 10.1 - - - -
259D ALA* 4.2 2.9 - - - +
263D ASN* 2.5 34.8 + - - -
318D ARG* 3.9 1.1 - - - -
663D ASP* 1.3 72.3 - - - +
665D VAL* 1.3 69.9 + - - +
668D GLU* 2.7 66.2 + - - +
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Residues in contact with VAL 665 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D VAL* 3.8 25.6 - - + +
206D GLU* 3.4 33.2 - - + -
207D VAL* 4.1 16.2 - - + -
299D TYR* 3.8 26.2 - - + +
316D LEU* 6.4 0.2 - - + -
320D GLN* 2.6 35.2 + - - +
663D ASP* 3.4 3.8 - - - +
664D SER* 1.3 77.3 + - - +
666D TYR* 1.3 58.5 + - - +
669D ARG* 3.3 28.7 + - - +
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Residues in contact with TYR 666 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D GLU* 3.4 26.5 - - - +
357D PHE* 4.5 7.5 - + - -
547D TYR* 5.2 1.4 + - - -
549D GLY* 4.8 0.5 - - - -
550D PRO* 3.2 26.0 + - - +
598D LEU* 5.5 1.1 - - + -
631D TYR* 3.6 2.4 - + - -
659D TRP* 3.9 12.6 - + - -
662D TYR* 3.4 20.2 - + + -
663D ASP* 3.0 18.7 + - - +
665D VAL* 1.3 76.0 - - - +
667D THR* 1.3 70.3 + - - +
669D ARG* 3.3 20.0 + - - +
670D TYR* 3.1 55.0 - + - -
801D 8VU 3.4 53.1 - + + -
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Residues in contact with THR 667 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D ALA* 4.2 5.2 - - + -
598D LEU* 5.9 0.9 - - - -
659D TRP* 3.5 41.7 - - + +
662D TYR* 3.3 25.6 - - - +
663D ASP 2.7 23.4 + - - -
664D SER 4.1 0.2 - - - -
666D TYR* 1.3 81.8 - - - +
668D GLU* 1.3 60.0 + - - +
670D TYR* 3.0 6.8 + - - +
671D MET* 2.8 33.5 + - + +
683D TYR* 3.5 20.6 - - + +
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Residues in contact with GLU 668 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D ALA* 4.7 1.8 - - - -
260D GLY* 2.9 22.1 + - - +
299D TYR* 3.9 5.7 + - - -
318D ARG* 2.8 64.2 + - - +
319D ILE* 6.0 0.5 - - - -
320D GLN* 4.5 5.0 + - - +
664D SER* 2.7 34.0 + - - +
667D THR* 1.3 72.3 - - - +
669D ARG* 1.3 58.6 + - - +
672D GLY* 2.8 48.2 + - - +
673D LEU* 3.8 11.4 - - + +
683D TYR* 4.3 3.6 - - - +
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Residues in contact with ARG 669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D GLU* 3.5 18.2 + - - +
207D VAL* 5.4 0.8 - - - +
320D GLN* 2.7 33.9 + - + +
353D TRP* 3.6 46.1 - - + +
354D VAL 5.7 0.4 - - - -
356D ARG 4.6 1.1 - - - -
357D PHE* 3.2 41.0 + - - +
595D ASN* 4.3 3.5 + - - -
665D VAL* 3.3 48.8 + - - +
666D TYR* 3.3 19.6 + - - +
667D THR 3.1 0.8 + - - -
668D GLU* 1.3 80.1 - - - +
670D TYR* 1.3 90.4 + - + +
801D 8VU 6.0 0.2 - - - -
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Residues in contact with TYR 670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D TRP* 3.5 44.4 - + + -
356D ARG 4.2 3.0 + - - -
357D PHE* 3.5 23.0 - - - -
550D PRO* 3.5 31.1 + - + +
551D CYS* 5.7 0.2 - - - +
594D ILE* 4.4 1.1 - - + +
595D ASN* 4.0 7.3 + - - +
596D ARG* 2.6 34.1 + - - -
598D LEU* 4.0 23.1 - - + -
666D TYR* 3.1 56.7 - + - -
667D THR* 3.0 4.9 + - - +
669D ARG* 1.3 103.7 + - - +
671D MET* 1.3 58.1 + - - +
672D GLY 3.8 0.7 - - - -
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Residues in contact with MET 671 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596D ARG* 3.7 5.4 - - - +
597D ARG 3.7 11.7 - - - -
598D LEU* 3.4 51.4 - - + +
659D TRP* 4.8 5.4 - - + -
667D THR* 2.8 18.7 + - + +
670D TYR* 1.3 78.6 - - - +
672D GLY* 1.3 65.8 + - - +
679D ASN* 2.5 45.8 + - - +
682D HIS* 3.8 32.8 - - + +
683D TYR* 3.3 28.0 - - + +
686D SER* 4.4 6.7 - - - +
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Residues in contact with GLY 672 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D ILE* 6.5 0.2 - - - -
596D ARG* 4.6 5.5 - - - +
668D GLU* 2.8 34.6 + - - +
670D TYR 3.8 0.6 - - - -
671D MET* 1.3 77.7 - - - +
673D LEU* 1.4 63.0 + - - -
678D ASP* 4.0 9.2 - - - -
683D TYR* 2.5 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