Contacts of the strand formed by residues 416 - 423 (chain A) in PDB entry 2WIN
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 416 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A ILE* 4.4 2.2 - - - -
401A THR* 3.3 25.3 - - - +
402A VAL 3.4 9.1 + - - -
403A ARG* 4.0 25.5 + - - +
414A GLN 4.1 2.4 + - - +
415A ALA* 1.3 75.8 - - - +
417A ARG* 1.3 74.2 + - - +
418A THR* 4.9 0.7 + - - +
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Residues in contact with ARG 417 (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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333A ILE* 3.8 34.9 + - + +
334A HIS* 4.2 17.2 + - - +
335A PHE* 3.4 38.9 - - + +
401A THR* 3.6 1.0 - - - +
402A VAL 3.2 27.7 + - - -
416A THR* 1.3 79.6 + - - +
418A THR* 1.3 77.9 + - - +
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Residues in contact with THR 418 (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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335A PHE* 4.2 2.6 - - - -
399A SER* 3.8 13.9 - - - +
400A ILE 3.4 12.3 - - - +
401A THR* 2.9 27.3 + - - +
416A THR* 4.9 0.3 + - - -
417A ARG* 1.3 89.6 + - - +
419A MET* 1.3 71.2 + - - +
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Residues in contact with MET 419 (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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335A PHE* 3.5 45.9 - - + -
338A THR* 3.7 27.8 - - + -
339A PRO 4.8 1.1 - - - +
340A LYS* 4.8 17.9 - - - -
348A PHE* 3.7 20.6 - - + -
350A LEU* 4.1 18.4 - - + -
399A SER* 3.7 3.1 + - - -
400A ILE* 3.1 45.4 + - + +
418A THR* 1.3 80.2 - - - +
420A GLN* 1.3 65.6 + - - +
421A ALA* 5.3 2.7 - - + -
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Residues in contact with GLN 420 (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 LYS* 4.1 16.0 - - - +
397A PRO* 3.5 32.4 - - + +
398A LEU 3.6 8.7 - - - +
399A SER* 5.2 5.2 - - - -
419A MET* 1.3 80.1 - - - +
421A ALA* 1.3 62.5 + - - +
422A LEU* 3.8 16.7 + - + +
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Residues in contact with ALA 421 (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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339A PRO 4.8 0.2 - - - +
340A LYS* 3.5 19.1 - - - +
341A TYR 4.2 2.0 - - - +
342A PHE* 3.3 24.4 - - + +
348A PHE* 4.5 13.0 - - + -
397A PRO* 3.6 3.8 - - - +
398A LEU 2.9 37.8 + - - +
400A ILE* 4.6 10.5 - - + +
419A MET* 4.3 3.5 - - + -
420A GLN* 1.3 73.8 - - - +
422A LEU* 1.3 62.5 + - - +
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Residues in contact with LEU 422 (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 LYS 3.1 8.1 + - - +
341A TYR* 3.2 35.3 - - + +
342A PHE* 3.1 19.3 + - - -
397A PRO* 3.9 16.2 - - + -
420A GLN* 3.8 30.3 - - + +
421A ALA* 1.3 79.4 - - - +
423A PRO* 1.3 75.6 - - + +
611A LYS* 6.2 0.7 - - + -
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Residues in contact with PRO 423 (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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341A TYR* 4.6 2.8 - - - -
342A PHE* 3.4 32.0 - - + +
344A PRO* 3.8 10.1 - - + -
395A GLN* 3.3 51.8 - - - +
396A LYS 4.1 0.9 - - - +
397A PRO* 4.2 10.1 - - + -
422A LEU* 1.3 97.6 - - + +
424A TYR* 1.3 62.1 + - - +
425A SER* 3.3 4.9 + - - -
611A LYS* 4.0 5.0 - - - +
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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