Contacts of the helix formed by residues 498 - 507 (chain C) in PDB entry 1T9D
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 GLY 498 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497C VAL* 1.3 79.2 - - - +
499C GLN* 1.3 66.5 + - - -
500C HIS* 3.4 2.5 - - - -
501C GLN* 3.1 25.1 + - - +
502C MET* 3.3 5.9 + - - +
582C MET* 3.3 22.9 - - - +
2701C FAD 4.5 0.7 - - - -
3702C P22 3.5 18.4 - - - -
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Residues in contact with GLN 499 (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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498C GLY* 1.3 67.0 - - - -
500C HIS* 1.3 60.7 + - - +
502C MET* 2.8 19.9 + - - +
503C TRP* 2.9 36.2 + - + -
577C ASN* 3.9 9.7 + - - -
579C GLU* 4.8 3.3 - - - +
581C GLY* 3.0 29.3 + - - -
582C MET* 3.4 25.7 - - - +
584C THR* 5.1 0.4 + - - -
585C GLN* 2.8 27.1 - - - +
648C LYS* 5.4 1.0 - - - +
649C VAL 2.7 33.8 + - - +
650C PRO* 3.9 0.2 - - - +
651C VAL* 3.6 12.5 - - + +
3702C P22 2.8 11.9 + - - +
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Residues in contact with HIS 500 (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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477C ILE* 4.9 0.9 - - - +
496C GLY* 3.0 40.5 - - - -
497C VAL 3.4 21.2 + - - -
498C GLY 4.4 0.2 - - - -
499C GLN* 1.3 78.3 - - - +
501C GLN* 1.3 73.0 + - + +
503C TRP* 3.7 13.6 - - + +
504C ALA* 3.1 24.6 + - - +
547C ILE* 3.2 21.9 + - + +
548C ASP 3.7 4.8 - - - +
549C GLY* 3.2 24.5 + - - -
575C LEU* 3.8 26.0 - - + -
3702C P22 3.1 37.8 + - - +
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Residues in contact with GLN 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C LEU* 4.3 6.1 - - + +
495C THR* 3.7 15.3 - - - +
496C GLY 3.4 17.5 + - - +
497C VAL* 3.3 2.0 - - - +
498C GLY 3.1 30.4 + - - +
499C GLN 3.0 0.8 - - - -
500C HIS* 1.3 87.1 + - + +
502C MET* 1.3 70.8 + - + +
504C ALA* 3.6 4.0 + - - +
505C ALA* 3.2 20.8 + - - +
516C PHE* 4.6 3.6 - - + -
518C THR* 2.7 26.8 + - - +
519C SER 3.1 23.4 + - - -
2701C FAD 3.3 26.6 - - - +
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Residues in contact with MET 502 (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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335C LEU* 3.9 22.4 - - + -
351C MET* 5.7 3.4 - - - +
355C HIS* 3.8 22.2 - - + -
498C GLY 3.6 0.9 - - - +
499C GLN 2.8 7.6 + - - +
501C GLN* 1.3 93.8 - - + +
503C TRP* 1.3 59.2 + - - +
504C ALA 3.1 1.6 - - - -
505C ALA* 3.1 5.0 + - + +
506C GLN* 2.8 35.4 + - - +
582C MET* 3.6 28.3 - - + -
651C VAL* 3.8 18.4 - - + -
2701C FAD 3.4 47.3 - - + +
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Residues in contact with TRP 503 (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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473C PRO* 3.4 35.9 - - + -
474C GLN* 3.5 37.8 + - + +
477C ILE* 3.6 15.8 - - + +
499C GLN* 2.9 45.7 + - + +
500C HIS* 3.7 11.2 - - + +
502C MET* 1.3 76.0 - - - +
504C ALA* 1.3 57.9 + - - +
506C GLN* 3.6 20.2 - - - -
507C HIS* 2.9 39.3 + + + +
575C LEU* 4.7 2.2 - - + -
577C ASN* 5.0 5.8 - - - -
645C VAL* 6.0 0.2 - - + -
646C ASP 6.0 0.4 - - - -
649C VAL* 3.3 33.2 - - + -
650C PRO 3.9 4.0 + - - -
651C VAL* 3.5 28.6 - - + +
652C LEU 5.0 0.8 - - - +
3702C P22 4.9 2.0 - - - -
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Residues in contact with ALA 504 (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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477C ILE* 3.7 12.5 - - - +
493C VAL* 5.5 0.2 - - + -
495C THR* 4.1 15.9 - - + -
500C HIS 3.1 20.4 + - - +
501C GLN 3.6 6.3 - - - +
502C MET 3.1 0.2 - - - -
503C TRP* 1.3 79.9 - - - +
505C ALA* 1.3 59.1 + - - +
508C TRP* 3.0 30.8 + - - +
510C TRP* 3.6 5.6 - - + -
516C PHE* 4.9 3.6 - - + -
547C ILE* 3.8 25.6 - - + -
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Residues in contact with ALA 505 (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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335C LEU* 3.4 33.4 - - + -
338C LEU* 3.7 15.5 - - + +
350C ASP* 4.8 2.9 - - - +
351C MET* 3.5 17.0 - - + +
501C GLN 3.2 7.4 + - - +
502C MET* 3.1 10.6 + - + +
504C ALA* 1.3 80.9 - - - +
506C GLN* 1.3 62.1 + - + +
510C TRP* 3.3 18.7 + - - +
516C PHE* 4.0 6.0 - - + -
3696C K 3.9 4.3 - - - -
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Residues in contact with GLN 506 (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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351C MET* 5.8 4.3 - - - -
355C HIS* 2.7 33.7 + - - +
460C TYR* 3.4 52.9 - - + +
502C MET* 2.8 19.8 + - - +
503C TRP* 3.6 26.0 - - - +
505C ALA* 1.3 78.8 - - + +
507C HIS* 1.3 66.7 + - + +
508C TRP 3.3 1.3 - - - -
651C VAL* 4.1 7.8 - - - +
652C LEU 3.5 25.6 + - - +
653C PRO* 4.3 0.2 - - - +
3696C K 2.7 24.5 - - - -
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Residues in contact with HIS 507 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460C TYR* 3.5 44.0 - + + +
462C TYR* 3.7 13.4 - + - +
474C GLN* 3.3 39.7 - - + +
477C ILE* 3.8 19.1 - - + +
478C LYS* 3.1 45.2 - - + +
481C SER* 4.4 2.4 - - - -
503C TRP* 2.9 30.3 + + - +
506C GLN* 1.3 78.7 + - + +
508C TRP* 1.3 57.8 + - - +
509C THR* 4.3 1.0 + - - -
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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