Contacts of the strand formed by residues 378 - 383 (chain A) in PDB entry 1OFD
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 378 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A CYS* 4.0 24.5 - - - -
356A ILE 3.6 7.0 - - - +
357A THR* 4.2 3.8 - - + +
373A LEU* 4.1 28.3 - - + +
374A PRO 4.2 2.7 - - - +
375A GLU* 3.8 27.9 - - + +
376A VAL 3.4 2.3 - - - +
377A ASP* 1.3 78.4 - - - +
379A VAL* 1.3 62.5 + - - +
380A GLU 3.4 23.1 - - - +
381A LYS* 3.9 32.5 - - + +
1351A SER* 3.6 14.0 + - - -
1352A PHE* 3.5 20.0 - - + -
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Residues in contact with VAL 379 (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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356A ILE* 2.8 18.7 + - + +
357A THR 4.0 14.4 - - - +
358A LYS* 4.1 21.8 - - + -
360A ASP* 5.9 0.9 - - - +
377A ASP 4.6 0.9 - - - +
378A ILE* 1.3 74.8 - - - +
380A GLU* 1.3 68.3 + - + +
1351A SER* 5.3 5.6 - - - +
1352A PHE* 3.7 20.3 - - - +
1357A ASN* 4.4 1.4 + - - +
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Residues in contact with GLU 380 (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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354A TYR* 3.1 24.0 + - + -
355A CYS* 3.6 1.9 - - - -
356A ILE* 3.0 42.9 + - + +
378A ILE* 3.4 8.8 - - - +
379A VAL* 1.3 88.2 - - + +
381A LYS* 1.3 73.0 + - - +
382A GLY* 4.4 3.1 - - - +
401A LYS* 3.1 31.3 + - - -
1352A PHE* 4.9 0.4 - - - -
1356A ASP 5.6 2.0 - - - +
1357A ASN* 3.3 12.3 - - - +
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Residues in contact with LYS 381 (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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354A TYR 3.5 7.0 - - - +
355A CYS* 4.8 7.4 - - - -
375A GLU* 5.8 2.6 - - - +
378A ILE* 3.9 33.6 - - + +
380A GLU* 1.3 80.3 - - - +
382A GLY* 1.3 58.6 + - - +
1327A GLY 4.7 6.6 + - - +
1328A GLU* 3.0 44.4 + - + +
1346A PRO* 6.2 0.8 - - - +
1347A HIS* 4.9 14.3 - - - +
1352A PHE* 4.1 25.7 - - + -
1356A ASP 4.7 0.9 - - - +
1357A ASN* 2.7 20.1 + - + +
1358A VAL* 2.9 46.1 + - + +
1359A ILE* 6.5 0.2 - - + -
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Residues in contact with GLY 382 (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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353A ARG* 3.7 9.0 - - - -
354A TYR* 2.8 53.0 + - - +
380A GLU* 4.6 3.1 - - - -
381A LYS* 1.3 74.7 - - - +
383A ARG* 1.3 62.9 + - - +
1358A VAL* 3.8 10.5 - - - +
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Residues in contact with ARG 383 (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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344A LEU* 5.8 0.4 - - - +
348A GLY 5.8 0.2 + - - -
351A PRO* 6.2 0.4 - - - +
352A ALA 3.3 15.0 - - - +
353A ARG* 4.4 10.8 - - - +
354A TYR* 3.2 20.9 + - - -
382A GLY* 1.3 74.1 - - - +
384A LEU* 1.3 71.1 + - - +
385A ALA* 3.7 16.4 + - + +
388A GLN* 3.7 8.1 - - - +
1358A VAL* 3.8 25.5 - - + +
1360A ILE 5.4 0.4 + - - -
1361A GLY* 5.7 1.6 - - - -
1362A ASN* 2.9 27.3 + - - +
1379A ALA 4.1 4.7 - - - -
1380A GLY* 3.3 27.8 - - - +
1381A GLU* 2.7 40.2 + - - -
1398A GLY* 4.2 7.4 - - - -
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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