Contacts of the strand formed by residues 322 - 329 (chain B) in PDB entry 1U7V
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 TYR 322 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B PRO* 3.2 14.6 - - - +
321B GLU* 1.3 112.5 + - + +
323B TRP* 1.3 59.9 + - - +
324B CYS 3.9 5.8 - - - +
340B LYS* 3.5 47.5 + - + +
341B VAL 3.0 12.1 - - - +
342B PRO* 3.5 32.3 - - + -
343B SER* 3.6 2.9 - - - -
530B HIS* 2.9 38.9 + + + +
305C PRO 5.9 1.6 - - - -
306C SER* 6.0 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B PRO* 4.5 5.2 - - + -
322B TYR* 1.3 73.7 - - - +
324B CYS* 1.3 88.6 + - + +
341B VAL* 2.8 16.7 + - - +
342B PRO 3.2 23.6 - - - -
343B SER* 3.5 22.2 + - - +
345B CYS 2.9 22.0 + - - -
346B PRO* 3.6 8.2 + - + -
348B VAL* 4.0 6.7 - - + -
389B LEU* 3.2 47.1 - - + -
390B GLU 3.9 5.6 - - - -
391B CYS* 3.5 35.0 - - + -
397B VAL* 3.6 27.4 - - + -
527B ILE* 5.5 0.9 - - + -
529B LEU* 3.9 9.3 - - + +
530B HIS* 3.5 17.8 + - - -
531B ARG* 4.9 2.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B TYR* 3.3 6.2 + - - +
323B TRP* 1.3 112.6 - - + +
325B SER* 1.3 65.5 + - - +
326B ILE* 4.4 7.9 - - - -
340B LYS* 3.7 1.9 - - - -
341B VAL* 3.1 52.7 + - - +
348B VAL* 4.9 0.7 - - - -
389B LEU* 5.2 0.4 - - - -
527B ILE* 3.9 18.2 - - + -
528B HIS 3.0 15.0 - - - +
529B LEU* 3.9 2.2 - - + -
530B HIS* 3.8 5.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B CYS* 1.3 72.9 + - - +
326B ILE* 1.3 64.3 + - - +
327B ALA 4.2 0.2 - - - -
338B THR* 3.8 18.2 - - - +
339B PHE 3.3 5.6 - - - -
340B LYS* 4.5 6.9 - - - +
526B GLU 3.5 1.7 - - - +
527B ILE* 3.2 6.8 - - - -
528B HIS* 2.9 42.0 + - - +
530B HIS* 2.7 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B CYS* 4.4 3.6 - - - -
325B SER* 1.3 79.4 - - - +
327B ALA* 1.3 62.3 + - - +
328B TYR 4.1 1.4 + - - -
338B THR* 3.3 4.1 - - - +
339B PHE* 2.6 56.7 + - + +
341B VAL* 4.1 20.9 - - + -
348B VAL* 4.4 3.6 - - + -
350B VAL* 3.8 15.9 - - + -
362B PHE* 3.7 20.6 - - + -
389B LEU* 3.7 23.8 - - + -
525B ILE* 3.8 31.0 - - + -
526B GLU 3.6 3.6 - - - +
527B ILE* 4.3 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B SER 4.2 0.4 - - - -
326B ILE* 1.3 74.4 - - - +
328B TYR* 1.3 60.1 + - - +
329B PHE* 3.0 27.1 - - + -
334B GLN* 3.8 24.5 - - - +
338B THR* 4.0 10.3 - - + +
525B ILE* 3.2 3.7 - - - -
526B GLU* 3.0 37.2 + - + +
528B HIS* 6.1 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ILE 4.0 2.8 + - - -
327B ALA* 1.3 73.1 - - - +
329B PHE* 1.3 74.2 + - - +
330B GLU* 2.6 38.4 + - + +
334B GLN* 3.1 14.7 - - - +
335B VAL* 3.0 52.6 + - + +
337B GLU 5.6 1.4 + - - -
362B PHE* 4.1 14.4 - - + -
364B LEU* 3.7 27.1 - - + -
367B LEU* 3.3 30.5 - - + -
372B ARG* 4.5 0.4 - - - -
380B ARG* 2.9 22.9 + - - +
383B ILE* 5.1 0.2 - - + -
523B CYS* 3.3 22.7 - - + +
524B TRP 3.2 16.4 - - - -
525B ILE* 3.7 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ALA* 3.0 43.5 - - + -
328B TYR* 1.3 97.7 - - - +
330B GLU* 1.3 63.7 + - - +
331B MET 4.0 3.8 - - - +
333B VAL 3.3 10.5 - - - -
334B GLN* 3.7 37.2 - - + -
335B VAL* 4.1 1.1 - - - +
524B TRP* 2.8 63.4 + + + +
526B GLU* 4.0 19.1 - - + -
317C SER* 5.0 4.0 - - - -
319C VAL* 3.5 33.9 - - + -
----------------------------------------------------------
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