Contacts of the strand formed by residues 378 - 383 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B CYS* 3.5 36.3 - - - -
356B ILE 3.8 3.8 - - - +
357B THR* 4.3 2.0 - - + +
373B LEU* 4.2 20.2 - - + +
374B PRO 3.7 9.0 - - - +
375B GLU* 3.1 48.2 + - - +
376B VAL 4.8 0.7 - - - +
377B ASP* 1.3 78.6 - - - +
379B VAL* 1.3 62.7 + - - +
380B GLU 3.6 14.6 - - - +
381B LYS* 3.9 7.2 - - + -
1351B SER* 4.7 6.4 + - - -
1352B PHE* 3.5 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B ILE* 2.9 19.6 + - + +
357B THR 4.0 11.4 - - - +
358B LYS* 4.0 24.7 - - + +
360B ASP* 6.1 0.2 - - - +
377B ASP 3.5 0.6 + - - +
378B ILE* 1.3 74.7 - - - +
380B GLU* 1.3 69.6 + - + +
1352B PHE* 3.7 19.1 - - - +
1357B ASN* 4.2 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B TYR* 2.9 32.1 + - + -
355B CYS* 3.4 4.2 - - - -
356B ILE* 3.0 39.0 + - + +
378B ILE* 3.6 6.5 - - - +
379B VAL* 1.3 88.3 - - + +
381B LYS* 1.3 72.2 + - - +
382B GLY* 4.1 4.1 - - - +
401B LYS* 2.6 32.1 + - - -
1352B PHE* 5.3 0.4 - - - -
1356B ASP 5.8 0.9 - - - +
1357B ASN* 3.3 11.0 - - - +
1378B ARG* 5.2 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B TYR 3.5 5.4 - - - +
355B CYS* 4.1 10.8 - - + -
375B GLU* 2.9 36.1 + - - -
378B ILE* 3.9 22.0 - - + -
380B GLU* 1.3 78.3 - - - +
382B GLY* 1.3 59.4 + - - +
1327B GLY 4.7 6.1 + - - -
1328B GLU* 2.9 42.1 + - + +
1346B PRO* 6.0 1.0 - - - +
1347B HIS* 4.9 3.0 - - - +
1352B PHE* 3.8 20.3 - - + -
1357B ASN* 2.8 21.3 + - + +
1358B VAL* 2.9 44.8 + - + +
1359B ILE* 6.6 0.2 - - + -
1378B ARG* 3.8 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ARG* 3.6 10.0 - - - -
354B TYR* 2.8 51.2 + - - +
380B GLU* 4.1 5.5 - - - -
381B LYS* 1.3 74.3 - - - +
383B ARG* 1.3 62.5 + - - +
1358B VAL* 3.7 10.4 - - - +
1378B ARG* 4.4 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ALA 3.3 13.7 - - - +
353B ARG* 4.3 10.8 - - + +
354B TYR* 3.3 20.3 + - - -
382B GLY* 1.3 75.0 - - - +
384B LEU* 1.3 70.6 + - - +
385B ALA* 3.6 18.3 + - + +
388B GLN* 3.6 8.1 - - - +
1358B VAL* 3.8 26.0 - - + +
1360B ILE 5.5 0.2 + - - -
1361B GLY* 5.7 1.4 - - - -
1362B ASN* 2.8 30.5 + - - +
1378B ARG* 4.9 7.8 - - - +
1379B ALA 4.1 5.8 - - - -
1380B GLY* 3.3 26.8 - - - -
1381B GLU* 2.8 38.6 + - - +
1398B GLY* 4.1 7.5 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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