Contacts of the strand formed by residues 550 - 556 (chain B) in PDB entry 4YCV
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 THR 550 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LYS* 6.2 0.7 - - + -
315B ILE* 3.5 35.1 - - + +
348B TYR* 4.1 8.1 - - + -
349B TRP 3.1 37.7 - - - +
350B ALA 3.7 2.7 - - - +
352B ALA 3.6 9.6 - - - +
506B THR* 3.8 5.5 - - - -
507B GLU* 3.1 34.2 + - - +
509B ASN* 4.9 0.4 - - - +
547B LEU* 3.8 8.0 - - + +
548B PRO* 2.7 17.9 + - - +
549B PRO* 1.3 74.5 + - - +
551B GLY* 1.3 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B PHE* 4.1 0.3 - - - +
348B TYR* 3.5 6.3 - - - -
349B TRP* 2.9 36.0 + - - +
352B ALA 3.6 9.3 + - - -
357B LEU* 4.2 15.9 - - - +
505B TYR 3.4 12.3 - - - -
506B THR* 4.1 2.9 - - - -
507B GLU 4.1 1.6 - - - -
550B THR* 1.3 76.1 - - - +
552B GLY* 1.3 58.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 552 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B PHE* 3.2 11.2 - - - -
348B TYR* 3.6 20.5 - - - -
357B LEU* 3.9 4.3 - - - +
503B ASN 4.7 0.2 - - - -
504B ALA* 3.1 5.2 - - - +
505B TYR* 2.9 39.2 + - - +
507B GLU 5.0 0.6 - - - +
551B GLY* 1.3 75.8 - - - -
553B LEU* 1.3 62.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B CYS 4.8 0.2 - - - +
346B GLU* 3.1 7.8 - - - +
347B PHE* 2.9 63.7 + - + +
348B TYR* 4.9 3.4 - - - -
357B LEU* 4.2 8.1 - - + +
360B TRP* 3.8 17.7 - - + -
361B SER* 3.7 14.1 - - - +
502B LEU* 3.6 22.7 - - + -
503B ASN 3.3 6.3 - - - -
504B ALA* 3.5 13.9 - - + -
552B GLY* 1.3 75.0 - - - +
554B GLY* 1.3 73.2 + - - +
555B LEU* 3.7 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 554 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B CYS 3.2 10.1 - - - -
346B GLU* 3.8 13.7 - - - -
501B VAL 4.3 0.2 - - - +
502B LEU* 3.4 4.3 - - - -
503B ASN* 2.9 35.2 + - - -
553B LEU* 1.3 79.1 - - - +
555B LEU* 1.3 64.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 555 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LEU* 3.7 40.4 - - + -
344B SER* 3.1 12.7 - - - -
345B CYS* 2.9 36.4 + - + +
346B GLU* 4.9 0.6 - - - +
360B TRP* 4.3 9.0 - - + -
364B PHE* 4.1 12.3 - - + -
365B PHE* 4.4 10.1 - - + -
501B VAL 3.8 1.6 - - - -
502B LEU* 3.5 40.6 - - + -
553B LEU* 3.7 11.7 - - + -
554B GLY* 1.3 74.3 - - - -
556B GLY* 1.3 66.4 + - - +
557B ILE* 3.3 4.9 + - + +
560B ILE* 4.4 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 556 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B PHE* 5.3 8.5 - - - -
343B THR 4.3 3.4 - - - -
344B SER* 4.9 2.2 - - - -
500B GLU 5.6 0.4 - - - -
501B VAL 3.0 15.5 + - - +
554B GLY 4.3 0.2 - - - -
555B LEU* 1.3 70.9 - - - +
557B ILE* 1.3 61.6 + - - -
558B ASP* 3.5 3.4 - - - -
559B ARG* 4.3 13.0 - - - +
560B ILE* 3.1 30.7 + - - +
----------------------------------------------------------
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