Contacts of the helix formed by residues 498 - 508 (chain B) in PDB entry 1T9A
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497B VAL* 1.3 78.2 - - - +
499B GLN* 1.3 67.5 + - - -
500B HIS* 3.3 3.6 - - - -
501B GLN* 2.9 26.6 + - - +
502B MET* 3.1 9.3 + - - +
582B MET* 4.0 10.1 - - - -
698B P23 3.2 20.9 - - - -
1701B FAD 4.2 4.2 - - - +
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Residues in contact with GLN 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B GLY* 1.3 69.4 - - - -
500B HIS* 1.3 64.9 + - - +
502B MET* 2.8 5.5 + - - +
503B TRP* 2.8 46.7 + - + -
577B ASN* 3.8 9.7 + - - -
579B GLU* 4.8 2.6 - - - +
581B GLY* 3.1 29.0 + - - -
582B MET* 3.4 22.2 - - - +
584B THR* 5.4 0.8 + - - -
585B GLN* 2.8 25.6 + - - +
648B LYS* 5.9 0.4 - - - +
649B VAL 2.8 33.1 + - - +
650B PRO* 3.9 0.8 - - - +
651B VAL* 3.6 18.4 - - + +
698B P23 3.0 9.7 + - - +
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Residues in contact with HIS 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B ILE* 4.7 0.7 - - - +
496B GLY* 3.1 27.7 + - - -
497B VAL 3.2 34.5 + - - -
498B GLY 3.9 1.1 - - - -
499B GLN* 1.3 75.1 - - - +
501B GLN* 1.3 66.3 + - - +
503B TRP* 3.7 13.4 - - + +
504B ALA* 2.9 30.8 + - - +
547B ILE* 3.2 29.1 - - + +
548B ASP 3.4 9.6 - - - +
549B GLY* 3.3 17.3 + - - -
552B SER* 3.8 0.4 - - - -
575B LEU* 3.9 25.6 - - + -
698B P23 2.9 37.0 + - - +
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Residues in contact with GLN 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B LEU* 4.0 9.4 - - + +
495B THR* 3.5 15.9 - - - +
496B GLY 3.5 20.5 + - - +
497B VAL* 3.4 1.8 - - - +
498B GLY 2.9 27.0 + - - +
500B HIS* 1.3 85.6 - - - +
502B MET* 1.3 74.3 + - + +
504B ALA* 3.4 3.5 + - - +
505B ALA* 3.1 21.5 + - - +
516B PHE* 4.5 3.4 - - + -
518B THR* 2.6 25.3 + - - +
519B SER 3.0 24.5 + - - +
1701B FAD 3.3 24.2 - - - +
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Residues in contact with MET 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B LEU* 4.0 17.9 - - + -
351B MET* 4.7 6.5 - - - -
355B HIS* 4.0 28.0 - - + -
498B GLY 3.1 10.0 + - - +
499B GLN 2.8 7.2 + - - +
501B GLN* 1.3 101.2 - - + +
503B TRP* 1.3 59.3 + - - +
505B ALA* 3.1 4.4 + - - +
506B GLN* 2.9 35.8 + - + +
582B MET* 4.8 4.5 - - - -
651B VAL* 3.8 20.0 - - + -
1701B FAD 3.3 52.3 - - + +
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Residues in contact with TRP 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473B PRO* 3.4 35.7 - - + -
474B GLN* 3.5 30.9 - - + +
477B ILE* 3.5 16.1 - - + +
499B GLN* 2.8 47.5 + - + +
500B HIS* 3.7 11.2 - - + +
502B MET* 1.3 73.2 - - - +
504B ALA* 1.3 62.3 + - - +
506B GLN* 3.8 18.8 - - - -
507B HIS* 3.0 33.0 + + + +
575B LEU* 4.8 2.5 - - + -
577B ASN* 4.9 7.9 - - - -
645B VAL* 5.9 0.9 - - + -
646B ASP 5.8 0.4 - - - -
649B VAL* 3.2 44.9 - - + -
650B PRO 4.2 1.1 - - - -
651B VAL* 3.6 28.7 - - + +
652B LEU 4.9 1.0 - - - +
698B P23 4.9 2.2 - - - -
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Residues in contact with ALA 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B ILE* 3.8 12.1 - - - +
493B VAL* 5.3 0.4 - - + -
495B THR* 4.0 22.0 - - + -
500B HIS 2.9 19.5 + - - +
501B GLN 3.5 5.4 - - - +
502B MET 3.2 0.2 - - - -
503B TRP* 1.3 78.2 - - - +
505B ALA* 1.3 60.2 + - - +
508B TRP* 3.0 31.5 + - - +
510B TRP* 3.3 5.6 - - + -
516B PHE* 4.8 4.0 - - + -
547B ILE* 4.1 21.3 - - + -
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Residues in contact with ALA 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B LEU* 3.5 32.1 - - + -
338B LEU* 3.7 14.8 - - + +
350B ASP* 4.8 1.9 - - - +
351B MET* 4.3 11.2 - - + +
501B GLN 3.1 9.4 + - - +
502B MET* 3.1 11.6 + - - +
504B ALA* 1.3 78.4 - - - +
506B GLN* 1.3 60.2 + - - +
510B TRP* 2.9 32.1 + - - +
516B PHE* 4.1 2.4 - - + -
696B K 3.8 2.3 - - - -
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Residues in contact with GLN 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B ASP* 4.7 1.1 - - - -
351B MET* 4.8 5.6 - - + -
355B HIS* 2.6 35.9 + - - +
460B TYR* 3.4 51.1 - - + +
502B MET* 2.9 20.4 + - + +
503B TRP* 3.8 21.8 - - - -
505B ALA* 1.3 76.8 - - - +
507B HIS* 1.3 68.3 + - + +
508B TRP 3.3 1.1 - - - -
651B VAL* 4.2 6.8 - - - +
652B LEU 3.4 26.9 + - - +
696B K 2.6 25.3 - - - -
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Residues in contact with HIS 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B TYR* 3.4 41.3 - - + +
462B TYR* 3.8 16.0 - + - +
474B GLN* 3.5 31.5 - - + +
477B ILE* 3.7 18.3 - - + +
478B LYS* 3.8 43.2 + - + +
481B SER* 4.4 2.4 + - - -
503B TRP* 3.0 20.8 + + - +
506B GLN* 1.3 91.9 + - + +
508B TRP* 1.3 59.0 + - - +
509B THR* 4.2 1.9 + - - -
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Residues in contact with TRP 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B GLN* 3.2 3.3 - - - +
477B ILE* 3.9 11.7 - - + -
480B LEU* 3.9 19.5 - - + -
481B SER* 3.6 43.5 + - - -
484B ALA* 4.0 11.7 - - + -
491B VAL* 4.1 14.0 - - + +
493B VAL* 3.8 22.8 - - + +
504B ALA 3.0 21.7 + - - +
506B GLN 3.3 1.4 - - - -
507B HIS* 1.3 78.9 - - - +
509B THR* 1.3 86.5 + - - +
510B TRP* 3.4 40.4 + + + -
545B ILE* 4.3 5.8 - - + -
547B ILE* 3.8 28.7 - - + -
696B K 2.6 25.2 - - - -
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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