Contacts of the strand formed by residues 412 - 418 (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 ARG 412 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369B ILE* 3.8 13.6 - - + +
370B LEU 3.3 17.9 - - - +
371B LYS* 3.6 32.3 - - - +
372B LYS* 3.6 5.0 - - - +
408B GLN* 3.5 4.5 - - - +
409B THR* 2.9 32.3 + - - +
411B ASP* 1.3 105.8 + - - +
413B LEU* 1.3 63.7 + - - +
414B TYR* 3.5 31.7 - - + -
637B LEU* 3.7 25.0 - - - +
638B TPO 3.1 48.4 + - - -
639B PRO 5.0 0.8 + - - -
640B PRO* 5.5 0.6 - - - +
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Residues in contact with LEU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B LYS 4.3 0.2 - - - -
369B ILE* 3.2 8.1 - - - +
370B LEU* 2.8 40.5 + - + +
372B LYS* 4.1 12.3 - - + -
375B VAL* 4.4 14.8 - - + -
384B THR* 4.2 20.0 - - + -
407B PHE 4.0 1.3 - - - -
408B GLN* 3.8 12.1 - - + -
412B ARG* 1.3 74.4 - - - +
414B TYR* 1.3 68.1 + - - +
415B PHE* 4.7 2.5 - - + -
653B PHE* 3.6 39.3 - - + -
656B PHE* 3.5 42.6 - - + -
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Residues in contact with TYR 414 (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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336B LEU* 3.3 37.9 - - + +
341B PHE* 4.7 3.1 - + - -
367B ILE* 4.0 13.7 - - + -
368B LYS 3.2 5.4 - - - +
369B ILE* 3.7 31.2 - - + -
406B CYS* 3.1 5.9 - - - +
407B PHE* 2.9 70.5 + + + +
409B THR* 3.7 21.7 + - + -
411B ASP* 5.4 0.2 + - - -
412B ARG* 3.5 41.0 - - + +
413B LEU* 1.3 90.6 - - - +
415B PHE* 1.3 63.7 + - - +
637B LEU* 3.7 6.4 - - - +
656B PHE* 3.7 2.4 - - - -
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Residues in contact with PHE 415 (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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366B ALA 3.6 0.2 - - - +
367B ILE* 3.2 6.3 - - - -
368B LYS* 2.9 52.7 + - + -
370B LEU* 4.0 22.0 - - + -
384B THR* 4.0 17.9 - - + -
387B GLU* 4.1 15.0 - - + -
388B LYS* 3.9 31.9 - - + -
391B LEU* 3.7 19.3 - - + -
403B LEU* 4.5 2.0 - - + -
406B CYS* 3.8 14.1 - - + -
413B LEU* 4.7 0.4 - - + -
414B TYR* 1.3 79.6 - - - +
416B VAL* 1.3 61.2 + - - +
417B MET* 3.4 19.7 + - + +
656B PHE* 3.6 26.7 - + - -
901B LW4 5.7 0.4 - - + -
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Residues in contact with VAL 416 (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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334B VAL* 4.4 3.8 - - + -
339B PHE* 4.1 26.2 - - + -
365B TYR* 3.8 20.4 - - + -
366B ALA 3.9 2.5 - - - -
367B ILE* 4.2 13.2 - - + +
403B LEU* 3.7 1.6 - - - +
404B HIS* 2.6 62.8 + - + +
405B SER 2.9 21.6 + - - +
407B PHE* 3.8 27.1 - - + -
415B PHE* 1.3 72.5 - - - +
417B MET* 1.3 53.8 + - - +
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Residues in contact with MET 417 (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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365B TYR* 3.4 11.9 - - - +
366B ALA 2.7 31.3 + - - +
368B LYS 5.1 0.7 - - - +
391B LEU* 3.7 28.5 - - + -
401B THR* 3.5 28.7 - - - +
402B GLN 3.1 26.7 - - - +
403B LEU* 3.6 25.4 - - - -
404B HIS 4.8 0.2 - - - -
415B PHE* 3.8 14.6 - - + +
416B VAL* 1.3 73.5 - - - +
418B GLU* 1.3 68.0 + - - +
901B LW4 3.6 38.1 - - + +
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Residues in contact with GLU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B LEU 5.3 0.2 - - - -
365B TYR* 4.7 2.0 - - - -
366B ALA* 4.1 0.2 - - - +
400B LEU 3.3 2.9 - - - +
401B THR* 3.4 5.1 - - - -
402B GLN* 2.6 55.0 + - - +
417B MET* 1.3 72.9 - - - +
419B TYR* 1.3 61.4 + - - +
420B VAL* 4.2 11.6 - - + +
478B LYS* 2.8 41.7 + - - -
663B PHE* 3.6 31.0 - - + -
664B VAL 4.9 2.0 - - - +
901B LW4 2.8 26.5 + - - +
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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