Contacts of the strand formed by residues 403 - 408 (chain B) in PDB entry 3IW4
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 LEU 403 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B LYS* 4.5 1.8 - - + +
391B LEU* 3.6 45.8 - - + +
392B ALA* 3.9 4.9 - - + -
396B LYS* 4.0 5.4 - - - +
401B THR 3.7 2.8 + - - -
402B GLN* 1.3 71.6 - - - +
404B HIS* 1.3 62.1 + - - +
405B SER* 3.8 20.9 - - - +
406B CYS* 4.4 18.2 - - + +
415B PHE* 4.5 1.3 - - + -
416B VAL 3.8 6.7 - - - +
417B MET* 3.6 23.5 - - + +
658B TYR* 3.9 26.0 - - + -
660B ASN* 2.7 39.5 + - + +
663B PHE* 3.4 3.0 - - - -
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Residues in contact with HIS 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ASP* 3.5 30.6 + - - +
334B VAL* 3.4 30.5 - - + +
339B PHE* 5.6 0.2 - + - -
358B ARG* 5.2 3.8 + - - -
365B TYR* 4.2 17.7 + + + -
402B GLN 3.5 3.8 + - - -
403B LEU* 1.3 72.5 - - - +
405B SER* 1.3 77.6 + - - -
416B VAL* 2.6 41.8 + - + +
659B VAL* 4.4 1.6 - - + +
660B ASN* 2.8 30.5 + - - +
663B PHE* 3.4 42.0 - + + -
665B HIS* 4.4 4.6 - + - -
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Residues in contact with SER 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B VAL* 3.5 12.3 + - - +
403B LEU* 3.5 11.6 - - - -
404B HIS* 1.3 101.5 + - - +
406B CYS* 1.3 60.8 + - - +
407B PHE* 5.1 1.7 - - - -
416B VAL* 2.9 26.4 + - - +
658B TYR 3.1 20.0 - - - -
659B VAL* 3.5 21.9 - - - +
660B ASN 4.2 0.4 - - - +
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Residues in contact with CYS 406 (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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388B LYS* 3.6 21.8 - - - -
403B LEU* 4.4 10.3 - - + -
405B SER* 1.3 75.5 - - - +
407B PHE* 1.3 63.8 + - - +
414B TYR 3.1 18.2 - - - +
415B PHE* 3.8 15.7 - - + -
656B PHE* 3.4 30.7 - - + -
657B SEP 3.2 3.4 - - - +
658B TYR* 3.0 42.1 + - - +
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Residues in contact with PHE 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B VAL* 4.0 25.1 - - + +
335B LYS* 3.9 7.4 - - + -
336B LEU* 3.6 39.3 - - + -
339B PHE* 4.9 4.3 - + - -
367B ILE* 5.7 0.9 - - + -
405B SER* 4.9 1.3 - - - -
406B CYS* 1.3 81.5 - - - +
408B GLN* 1.3 73.2 + - - +
409B THR* 4.4 4.3 - - + -
414B TYR* 2.9 70.1 + + + +
416B VAL* 3.8 23.3 - - + -
656B PHE* 3.0 11.4 - - - -
657B SEP 3.8 19.3 - - - +
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Residues in contact with GLN 408 (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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372B LYS* 2.7 31.3 + - - +
407B PHE* 1.3 85.5 - - - +
409B THR* 1.3 69.8 + - - +
412B ARG 3.5 11.7 - - - +
413B LEU* 3.8 13.2 - - + -
414B TYR* 4.5 0.4 - - - -
650B GLN* 4.2 1.4 - - - +
653B PHE* 3.0 33.9 + - - +
655B GLY 5.2 0.8 - - - +
656B PHE* 3.9 11.9 - - + +
657B SEP 2.7 35.1 + - - +
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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