Contacts of the strand formed by residues 396 - 404 (chain B) in PDB entry 1IVV
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 ILE 396 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243B TRP* 3.4 32.8 - - + -
257B LEU* 6.1 0.2 - - + -
260B ILE* 4.1 15.9 - - + -
271B ILE* 3.7 31.0 - - + -
272B ILE* 4.2 16.6 - - + -
388B TRP* 5.0 15.0 - - + -
389B TYR 3.6 7.2 - - - +
390B LEU* 4.2 10.5 - - + -
394B GLY 4.1 1.3 - - - +
395B THR* 1.3 72.1 - - - +
397B GLU* 1.3 64.6 + - - +
512B TYR* 4.1 8.7 - - + -
609B PHE* 5.9 0.4 - - + -
610B LYS* 3.2 2.6 - - - +
611B LEU* 2.7 54.3 + - + +
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Residues in contact with GLU 397 (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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370B ARG* 5.0 0.7 - - - -
388B TRP* 3.5 8.7 - - - -
389B TYR* 2.7 55.4 + - + +
391B TYR* 2.6 43.4 + - + -
395B THR* 4.1 0.4 - - + -
396B ILE* 1.3 77.2 - - - +
398B PHE* 1.3 69.7 + - - +
399B GLU* 5.0 5.9 - - - +
517B HIS* 5.4 6.2 + - - -
609B PHE* 3.3 15.7 + - - +
610B LYS* 3.7 19.0 - - + +
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Residues in contact with PHE 398 (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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277B ILE* 3.7 26.2 - - + -
386B PHE* 3.7 20.9 - + + -
387B TYR 3.2 32.5 - - - -
388B TRP* 3.5 30.3 - + + -
397B GLU* 1.3 80.4 - - - +
399B GLU* 1.3 70.1 + - - +
400B ALA* 3.6 23.8 - - + -
435B PHE* 5.0 1.3 - + - -
588B PHE* 3.5 35.7 - + - -
608B GLY* 3.3 4.2 - - - -
609B PHE* 3.0 54.8 + + + +
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Residues in contact with GLU 399 (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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370B ARG* 5.0 3.1 + - - -
387B TYR* 2.8 42.4 + - - +
389B TYR* 2.7 43.3 + - + +
397B GLU* 5.0 6.4 - - - +
398B PHE* 1.3 81.4 - - - +
400B ALA* 1.3 70.0 + - - +
401B LYS* 3.5 20.9 + - + -
606B THR* 3.4 24.2 + - - +
607B VAL 3.5 9.4 - - - +
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Residues in contact with ALA 400 (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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384B TYR* 6.3 0.7 - - + -
385B GLY 3.5 6.7 - - - +
386B PHE* 5.6 0.4 - - + -
398B PHE* 3.6 19.6 - - + -
399B GLU* 1.3 74.4 - - - +
401B LYS* 1.3 60.4 + - - +
402B ALA* 4.1 0.6 + - - -
435B PHE* 3.5 39.3 - - + -
588B PHE* 4.6 0.2 - - + -
590B LEU* 5.4 0.7 - - - +
605B ASP 3.9 0.2 - - - +
606B THR* 3.3 8.1 - - - -
607B VAL* 2.9 35.5 + - + +
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Residues in contact with LYS 401 (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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349A TRP 5.1 3.2 + - - -
350A GLY* 4.8 6.7 - - - -
351A ILE* 4.8 15.3 + - + +
370B ARG* 5.8 1.8 - - - +
376B PHE* 4.1 6.6 - - + -
383B ASP 3.7 1.6 - - - +
384B TYR* 3.2 8.4 - - - +
385B GLY* 2.9 37.5 + - - +
387B TYR* 3.3 49.4 + - + +
389B TYR* 3.9 5.6 + - - -
399B GLU* 3.5 25.7 + - + -
400B ALA* 1.3 76.1 - - - +
402B ALA* 1.3 60.8 + - - +
435B PHE* 6.3 0.2 - - - -
604B VAL* 4.0 26.7 - - + -
605B ASP 3.6 3.6 - - - -
606B THR* 3.8 14.8 - - + -
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Residues in contact with ALA 402 (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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382B DAH 5.9 0.4 - - + -
384B TYR* 3.9 26.5 - - + -
400B ALA 4.1 1.0 - - - -
401B LYS* 1.3 71.4 - - - +
403B THR* 1.3 62.3 + - - +
433B HIS* 4.8 9.9 - - + +
435B PHE* 5.9 2.9 - - + -
590B LEU* 4.4 15.5 - - + -
602B MET* 3.2 22.4 - - + +
604B VAL* 3.4 1.7 - - - -
605B ASP 2.8 36.8 + - - +
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Residues in contact with THR 403 (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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353A ALA* 3.5 2.4 - - - -
354A LYS* 3.2 32.4 + - + +
376B PHE* 3.8 26.0 - - + -
382B DAH 2.7 34.1 - - - -
383B ASP* 2.9 26.2 + - + +
384B TYR* 4.9 0.2 - - - -
402B ALA* 1.3 77.1 - - - +
404B GLY* 1.3 59.4 + - - +
601B ILE* 5.1 0.2 - - - +
602B MET* 2.6 31.3 + - - -
604B VAL* 3.8 15.0 - - + -
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Residues in contact with GLY 404 (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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354A LYS 3.0 18.7 + - - -
355A HIS* 3.8 4.9 - - - -
381B ASN 3.7 0.9 - - - -
382B DAH 4.1 0.7 - - - -
383B ASP* 3.3 13.7 - - - -
403B THR* 1.3 86.1 + - - +
405B VAL* 1.3 64.0 + - - -
601B ILE* 3.2 6.3 - - - +
602B MET* 2.8 28.4 + - - +
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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