Contacts of the strand formed by residues 488 - 493 (chain X) in PDB entry 1T6B
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 THR 488 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229X ALA* 3.9 20.6 - - - +
257X ALA* 4.6 3.4 - - + -
484X ILE* 2.8 28.0 + - + +
485X GLN 4.1 0.9 + - - +
486X GLU 3.5 0.8 + - - -
487X THR* 1.3 86.0 - - - +
489X ALA* 1.3 60.4 + - - +
504X ARG* 2.9 46.8 + - + -
505X ILE 3.2 23.3 - - - +
506X ALA* 3.8 5.2 - - - +
507X ALA 4.2 1.1 - - - +
585X ALA* 3.9 2.9 - - - +
586X LYS* 2.9 23.2 + - - -
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Residues in contact with ALA 489 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488X THR* 1.3 73.9 - - - +
490X ARG* 1.3 60.5 + - - +
491X ILE* 4.0 0.4 + - + -
503X ARG 3.7 0.7 - - - +
504X ARG* 3.2 7.1 - - - -
505X ILE* 2.9 37.4 + - + +
507X ALA* 4.3 2.1 - - + +
583X LEU* 4.0 31.2 - - + -
584X ASN 3.4 21.2 + - - +
587X MET* 3.7 12.8 - - + +
589X ILE* 5.4 2.2 - - + -
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Residues in contact with ARG 490 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299X HIS* 3.7 9.6 + - - -
323X GLY 3.4 17.2 + - - -
324X PHE 3.9 6.7 + - - -
325X SER 3.2 28.9 + - - -
326X ASN* 3.5 19.2 + - - +
327X SER 5.8 0.2 + - - -
489X ALA* 1.3 72.7 - - - +
491X ILE* 1.3 59.8 + - - +
492X ILE* 3.6 24.7 - - + +
502X GLU* 3.4 47.2 + - + -
503X ARG 3.5 4.0 - - - +
504X ARG* 3.9 20.9 - - + +
587X MET 2.8 14.9 + - - +
588X ASN* 3.0 24.8 + - - +
589X ILE* 2.7 36.0 + - - +
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Residues in contact with ILE 491 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489X ALA 5.2 0.7 - - - +
490X ARG* 1.3 78.6 - - - +
492X ILE* 1.3 67.5 + - - +
493X PHE* 4.6 0.4 - - + +
502X GLU* 3.4 1.2 - - - -
503X ARG 2.9 41.3 + - - +
505X ILE* 3.7 24.9 - - + -
523X LEU* 4.5 9.2 - - + -
526X ALA* 3.9 14.1 - - + -
527X LEU* 3.8 20.9 - - + -
531X PHE* 3.5 26.8 - - + -
583X LEU* 4.6 5.8 - - + -
589X ILE* 3.3 19.5 - - + +
591X ILE* 3.7 27.4 - - + -
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Residues in contact with ILE 492 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297X ARG* 4.8 5.4 - - - +
299X HIS* 3.4 43.5 - - + +
322X ALA* 5.9 0.7 - - + -
490X ARG* 3.6 31.0 - - + +
491X ILE* 1.3 77.5 - - - +
493X PHE* 1.3 56.7 - - - +
500X LEU* 4.0 28.3 - - + -
501X VAL 3.4 7.9 - - - +
502X GLU* 4.1 10.8 - - + +
588X ASN* 5.7 1.8 - - + -
589X ILE 2.7 16.7 + - - +
590X LEU* 3.5 22.3 - - + +
591X ILE* 2.8 33.1 + - - +
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Residues in contact with PHE 493 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491X ILE* 4.0 1.5 + - + -
492X ILE* 1.3 75.6 - - - +
494X ASN* 1.3 65.7 + - - +
495X GLY* 3.6 21.3 + - - -
496X LYS* 4.7 3.3 + - + +
499X ASN 3.5 1.6 - - - +
500X LEU* 4.7 1.1 - - - -
501X VAL* 2.8 36.6 + - + +
531X PHE* 3.5 43.5 - + + -
533X PHE* 3.4 31.4 - + - -
542X TYR* 3.8 40.4 - + - -
550X PHE* 3.5 29.4 - + - -
591X ILE* 3.4 23.8 - - + -
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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