Contacts of the strand formed by residues 506 - 514 (chain B) in PDB entry 4U7C
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 LEU 506 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B PHE* 3.8 12.8 - - + -
424B GLU* 3.4 8.0 - - - -
425B ILE* 3.0 33.5 + - + +
431B GLN* 3.9 31.4 - - + +
460B LEU* 3.6 37.7 - - + -
461B LYS 3.6 14.4 - - - +
462B ASN* 4.4 7.0 - - + -
463B VAL* 4.1 1.2 - - - +
492B LEU* 5.3 0.9 - - + -
504B LEU* 3.9 22.4 - - + -
505B ARG* 1.3 78.2 - - - +
507B ARG* 1.3 60.0 + - - +
508B LEU 4.1 9.9 - - - +
509B MET* 4.5 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B THR* 3.3 21.0 + - - +
422B PHE* 2.9 43.1 + - - +
424B GLU* 5.1 1.1 - - - +
461B LYS* 2.9 26.4 + - + +
462B ASN 3.6 17.7 - - - +
463B VAL* 4.3 14.2 + - + +
465B PHE* 3.3 38.6 - - - -
505B ARG 4.0 0.6 + - - -
506B LEU* 1.3 74.2 - - - +
508B LEU* 1.3 62.2 + - + +
4T G 2.5 41.4 + - - -
5T VKJ 2.8 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 508 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B GLU* 3.8 18.4 - - + +
420B ARG 3.2 13.7 - - - +
421B THR* 3.2 20.0 - - - +
422B PHE* 3.6 4.9 - - - -
459B LYS* 4.1 29.4 - - + -
460B LEU* 4.0 2.1 - - - -
461B LYS* 3.3 62.2 + - + +
506B LEU* 4.1 6.8 - - - +
507B ARG* 1.3 83.8 - - + +
509B MET* 1.3 78.2 + - - +
5T VKJ 5.5 2.5 - - + -
6T C 3.5 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 509 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B GLU* 3.2 1.4 - - - +
420B ARG* 2.9 30.9 + - - +
422B PHE* 3.6 16.1 - - + -
431B GLN* 3.9 14.6 - - - +
434B LEU* 4.3 7.9 - - + -
435B CYS* 3.4 44.4 - - + -
438B LEU* 3.5 17.3 - - + +
458B ILE* 5.5 4.7 - - + -
459B LYS 3.4 10.5 - - - +
460B LEU* 4.4 9.6 - - + -
492B LEU* 3.6 20.9 - - + -
506B LEU* 4.5 16.8 - - + -
508B LEU* 1.3 81.4 - - - +
510B GLY* 1.3 66.9 + - - +
511B VAL* 5.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 510 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B VAL 3.2 11.7 - - - -
419B GLU* 3.6 9.6 - - - -
438B LEU* 4.0 2.7 - - - -
458B ILE* 3.4 4.3 - - - +
459B LYS* 2.9 40.3 + - - +
509B MET* 1.3 78.6 - - - +
511B VAL* 1.3 70.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 511 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B SER* 3.3 3.0 - - - -
418B VAL* 2.9 33.0 + - + +
435B CYS* 4.3 15.5 - - - -
438B LEU* 4.0 26.8 - - + +
439B CYS* 4.1 17.5 - - - +
442B LEU* 3.9 13.4 - - + +
456B VAL* 4.3 10.8 - - + -
457B THR 3.5 7.0 - - - +
458B ILE* 4.4 7.9 - - + -
484B ILE* 3.9 28.7 - - + -
488B ALA* 4.8 0.7 - - + -
509B MET* 5.2 1.6 - - + -
510B GLY* 1.3 78.7 - - - +
512B ARG* 1.3 64.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B SER* 3.4 28.8 + - - -
416B MET 3.4 12.3 - - - +
417B SER* 3.6 14.6 + - - -
442B LEU* 4.2 2.9 - - - -
456B VAL* 3.3 6.1 - - - +
457B THR* 2.6 58.0 + - + +
459B LYS* 6.5 1.1 - - + -
511B VAL* 1.3 78.0 - - - +
513B ILE* 1.3 69.3 + - - +
514B SER* 5.0 7.7 + - - +
8T G 3.9 24.0 + - - -
9T A 4.1 7.5 + - - +
10T T 3.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 513 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B SER* 3.4 2.3 - - - -
416B MET* 2.9 42.5 + - + +
442B LEU* 3.7 17.2 - - + +
446B LEU* 3.8 40.6 - - + -
453B GLY* 3.8 18.6 - - - +
455B THR 3.2 13.0 - - - +
456B VAL* 4.1 11.0 - - + -
478B VAL* 3.8 26.9 - - + +
484B ILE* 4.7 4.9 - - + -
512B ARG* 1.3 75.0 - - - +
514B SER* 1.3 72.1 + - - +
516B PHE* 4.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 514 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B LYS 3.6 12.3 - - - -
415B SER* 4.2 8.3 - - - -
453B GLY* 3.5 3.5 - - - -
454B ARG 3.0 19.6 + - - -
455B THR* 2.8 27.2 + - - +
457B THR* 4.8 4.7 + - - -
512B ARG* 5.0 8.1 + - - +
513B ILE* 1.3 77.4 - - - +
515B SER* 1.3 73.5 + - - +
516B PHE* 3.5 13.2 - - - -
----------------------------------------------------------
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