Contacts of the strand formed by residues 403 - 410 (chain A) in PDB entry 1N8T
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 CYS 403 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A GLN* 4.0 0.2 - - - -
336A ALA* 3.6 19.3 - - + -
338A LEU* 4.0 13.9 - - + -
394A ILE* 4.3 20.2 - - - -
401A ILE* 3.2 21.2 + - - -
402A PRO* 1.3 73.1 - - - +
404A ASP* 1.3 63.0 + - - +
405A PHE* 3.5 26.5 - - + -
435A LEU* 5.2 0.7 - - - -
472A PRO 3.5 6.1 + - - -
473A THR* 3.1 14.1 - - + +
474A ASN 2.9 24.8 + - - -
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Residues in contact with ASP 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 5.1 3.5 - - - +
335A GLN* 3.7 17.3 + - - +
336A ALA 2.9 13.2 + - - +
337A VAL* 4.6 4.8 - - + +
338A LEU* 3.0 29.6 + - - +
403A CYS* 1.3 74.9 - - - +
405A PHE* 1.3 61.0 + - - +
406A LEU* 3.8 6.4 - - + +
474A ASN* 3.0 35.6 - - - +
476A ILE* 4.3 6.6 - - + +
493A TYR* 2.8 39.7 + - - +
496A LYS* 4.7 5.8 + - - -
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Residues in contact with PHE 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A LEU* 3.6 19.3 - - + -
340A TYR* 3.6 27.1 - + - -
391A TYR* 3.5 26.0 - + - -
394A ILE* 6.3 0.4 - - + -
403A CYS* 3.5 27.4 - - + -
404A ASP* 1.3 78.0 - - - +
406A LEU* 1.3 60.7 + - - +
428A PHE* 3.5 23.3 - + + -
431A GLN* 3.7 20.2 - - + -
432A THR* 3.7 22.0 - - + -
435A LEU* 4.1 11.7 - - + -
473A THR* 4.1 12.6 - - + -
474A ASN 2.8 16.9 + - - +
475A SER* 3.4 1.1 - - - +
476A ILE* 2.7 27.9 + - - +
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Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A VAL* 4.1 17.5 - - + -
338A LEU 3.3 12.9 + - - +
339A PRO* 3.6 12.1 - - + +
340A TYR* 2.7 30.8 + - - +
341A ASP* 5.4 0.2 - - - +
344A LEU* 5.5 2.2 - - + -
347A PHE* 4.3 18.8 - - + -
404A ASP 3.8 13.7 - - - +
405A PHE* 1.3 79.2 - - - +
407A ILE* 1.3 63.7 + - - +
428A PHE* 3.5 2.8 - - - -
476A ILE* 3.2 30.1 - - + +
478A PHE* 3.9 15.9 - - + -
489A LEU* 4.9 8.5 - - + -
492A MET* 5.3 0.2 - - + -
493A TYR* 3.7 28.3 - - + +
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Residues in contact with ILE 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A TYR* 3.4 21.8 - - + +
406A LEU* 1.3 75.7 - - - +
408A PRO* 1.3 80.6 - - + +
421A HIS* 4.4 2.5 - - + -
424A LEU* 4.2 10.8 - - + -
425A LEU* 3.5 39.5 - - + -
428A PHE* 3.6 46.2 - - + -
476A ILE 3.1 7.3 + - - -
477A VAL* 3.3 12.6 - - + +
478A PHE* 3.1 29.4 + - - -
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Residues in contact with PRO 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A TYR 4.1 4.7 - - - +
341A ASP* 3.7 27.8 - - + +
407A ILE* 1.3 98.5 - - + +
409A VAL* 1.3 59.3 + - - +
410A GLN 3.6 17.0 - - - +
411A THR* 5.4 2.0 - - - -
421A HIS* 2.9 30.7 + - + -
478A PHE* 3.0 30.5 - - + +
480A LYS* 4.1 0.7 - - - -
481A LEU* 3.8 20.0 - - + +
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Residues in contact with VAL 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A ILE 3.8 0.6 + - - -
408A PRO* 1.3 70.3 - - - +
410A GLN* 1.3 58.7 + - - +
421A HIS* 2.8 23.3 + - - -
425A LEU* 4.2 11.9 - - - +
477A VAL* 3.4 27.1 - - + +
478A PHE 2.9 16.2 + - - +
479A THR* 3.5 7.9 - - - +
547B PHE* 4.2 4.5 - - + -
548B ILE* 3.4 40.8 - - + +
551B GLN* 3.9 16.8 - - + +
552B ARG* 3.6 25.5 - - + +
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Residues in contact with GLN 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A PRO* 3.6 18.9 - - - +
409A VAL* 1.3 75.5 - - - +
411A THR* 1.3 62.2 + - - +
412A GLN* 4.2 0.7 + - - +
421A HIS* 3.9 2.0 - - - -
479A THR* 2.8 30.1 + - - +
480A LYS* 3.6 35.2 + - + +
481A LEU 4.6 0.3 + - - -
551B GLN 3.2 22.8 + - - +
552B ARG* 3.7 16.4 + - + +
554B ALA 2.5 30.8 + - - +
555B LYS* 4.3 9.1 + - - +
556B ILE* 3.8 8.0 - - - +
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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