Contacts of the strand formed by residues 407 - 412 (chain B) in PDB entry 4WMJ
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 407 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B HIS* 4.6 0.2 - - - -
340B ALA* 3.3 17.5 - - - +
342B LEU* 3.7 24.0 - - + -
398B VAL* 4.2 17.9 - - - -
405B ILE* 3.3 21.3 + - - -
406B PRO* 1.3 73.0 - - - +
408B ASP* 1.3 63.9 + - - +
409B PHE* 3.6 24.7 - - + -
439B LEU* 5.0 3.4 - - - -
476B PRO 3.5 5.7 + - - -
477B THR* 3.2 11.2 - - + +
478B ASN 3.0 23.9 + - - +
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Residues in contact with ASP 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LEU* 4.8 5.0 - - - +
339B HIS* 3.1 28.5 + - - -
340B ALA 2.9 6.5 + - - -
341B LEU* 3.6 7.3 - - + +
342B LEU* 2.8 32.4 + - - +
407B CYS* 1.3 72.2 - - - +
409B PHE* 1.3 57.7 + - - +
410B LEU* 3.7 5.3 - - + +
478B ASN* 2.9 38.0 - - + +
480B ILE* 4.7 6.1 - - + -
497B TYR* 2.7 38.6 + - - +
500B LYS* 4.6 1.6 + - - -
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Residues in contact with PHE 409 (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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342B LEU* 3.4 20.2 - - + -
344B TYR* 3.5 42.0 - + - -
395B TYR* 3.7 13.2 - + - -
407B CYS* 3.6 24.9 - - + -
408B ASP* 1.3 72.3 - - - +
410B LEU* 1.3 62.0 + - - +
432B PHE* 3.6 22.5 - + + -
435B GLN* 3.6 20.4 - - + -
436B THR* 3.5 23.3 - - + -
439B LEU* 4.0 11.9 - - + -
477B THR* 3.7 20.4 - - + -
478B ASN 2.9 10.1 + - - +
479B SER* 3.4 2.8 - - - +
480B ILE* 2.9 24.8 + - - +
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Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 4.9 1.6 - - - -
342B LEU 3.2 9.9 + - - +
343B PRO* 3.8 26.9 - - + -
344B TYR* 2.7 33.7 + - - +
348B LEU* 5.8 1.8 - - + -
351B PHE* 4.4 21.5 - - + -
408B ASP* 3.7 20.0 - - + +
409B PHE* 1.3 77.9 - - - +
411B ALA* 1.3 61.3 + - - +
432B PHE* 3.7 2.0 - - - -
480B ILE* 3.2 42.0 - - + +
485B PHE* 4.4 12.3 - - + -
493B LEU* 4.4 15.7 - - + -
497B TYR* 4.2 15.3 - - + +
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Residues in contact with ALA 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A LEU* 5.5 0.7 - - + -
344B TYR* 4.2 7.2 - - + -
410B LEU* 1.3 76.7 - - - +
412B PRO* 1.3 72.7 - - + +
429B LEU* 3.9 13.9 - - + -
432B PHE* 3.6 35.0 - - + -
480B ILE 2.9 7.5 + - - -
481B VAL* 3.2 8.8 - - - +
482B VAL* 3.1 22.9 + - - +
485B PHE* 4.1 7.5 - - - -
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Residues in contact with PRO 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A LEU* 4.4 4.0 - - - -
344B TYR 3.8 13.0 - - - +
345B ASP* 4.1 8.3 - - - +
411B ALA* 1.3 89.6 - - + +
413B ALA* 1.3 58.9 + - - +
414B GLN 3.4 20.0 - - - +
415B THR* 5.3 1.1 - - - -
425B HIS* 2.9 35.9 + - + -
429B LEU* 3.5 6.8 - - + +
482B VAL* 3.3 13.9 - - + +
484B LYS* 4.0 8.1 - - - -
485B PHE* 3.5 32.1 - - + +
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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