Contacts of the helix formed by residues 554 - 560 (chain 2) in PDB entry 5U8T
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 LYS 554 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5502 SER 4.6 0.7 - - - +
5512 GLN* 3.9 7.9 + - - +
5522 ILE 3.2 1.2 - - - -
5532 LEU* 1.3 85.7 - - + +
5552 TYR* 1.3 65.4 + - - +
5562 VAL 3.1 1.8 - - - -
5572 GLU* 3.6 36.8 + - + +
5582 LYS* 4.3 4.7 + - - +
5636 ILE* 3.8 35.1 - - + +
5646 LYS* 6.1 1.2 - - - +
6576 GLU* 4.4 13.8 + - - -
6586 GLN* 3.2 66.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 555 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5002 SER 3.3 14.6 + - - -
5012 MET* 3.0 49.4 - - + +
5032 PRO* 3.5 19.7 - - + +
5052 ILE* 4.9 3.6 - - + -
5152 VAL* 5.8 2.9 - - + -
5192 LEU* 5.9 0.7 - - + -
5512 GLN 4.2 1.8 + - - -
5522 ILE* 3.1 18.2 + - + +
5542 LYS* 1.3 81.1 - - - +
5562 VAL* 1.3 56.6 + - + +
5572 GLU 3.3 0.2 + - - -
5582 LYS* 3.7 4.0 + - + +
5592 THR* 2.2 58.2 + - + -
7602 GLN* 2.9 38.7 + - - +
7632 LEU* 3.7 10.1 - - + +
5626 GLY* 4.4 16.8 - - - -
5636 ILE* 4.6 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 556 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5152 VAL* 4.4 16.6 - - + -
5192 LEU* 3.6 25.8 - - + -
5522 ILE 4.1 6.3 - - - +
5532 LEU* 3.2 20.2 - - - +
5542 LYS 3.1 0.4 - - - -
5552 TYR* 1.3 78.6 - - + +
5572 GLU* 1.3 55.9 + - - +
5592 THR* 3.5 6.5 - - - -
5602 ALA* 2.4 45.3 + - + +
5632 ALA* 5.6 0.4 - - + -
6032 VAL* 5.0 9.0 - - + -
6052 LEU* 3.7 17.9 - - + -
6472 ILE* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 557 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4592 ARG* 4.6 19.0 + - - +
5542 LYS* 3.6 30.2 + - + +
5552 TYR 3.3 0.6 - - - -
5562 VAL* 1.3 78.4 - - - +
5582 LYS* 1.3 59.5 + - - +
5602 ALA* 3.0 25.1 - - - +
5632 ALA* 4.4 15.9 - - + +
5652 PHE* 3.1 45.6 - - + +
6052 LEU* 3.5 18.7 - - + +
6586 GLN* 4.8 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 558 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4592 ARG* 5.3 10.3 - - - +
5542 LYS 4.3 3.9 + - - +
5552 TYR* 3.7 5.4 + - + +
5572 GLU* 1.3 78.1 - - - +
5592 THR* 1.3 61.5 + - - +
5602 ALA 4.4 1.4 - - - +
7602 GLN* 5.5 2.9 - - - +
7642 MET* 4.7 17.3 - - - +
5616 GLU 4.1 20.2 - - - +
5626 GLY 4.5 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 559 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4742 PHE* 5.3 0.3 - - - -
5012 MET* 4.6 5.6 - - + -
5192 LEU* 3.5 33.4 - - + -
5552 TYR* 2.2 54.9 + - + -
5562 VAL* 3.2 9.2 - - - -
5572 GLU 2.9 0.8 - - - -
5582 LYS* 1.3 80.9 - - - +
5602 ALA* 1.3 67.1 + - - +
5612 HIS 3.6 0.9 + - - -
7632 LEU* 4.9 7.6 - - + -
7642 MET* 4.0 24.1 - - + +
7672 ILE* 4.6 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 560 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4742 PHE* 4.8 3.1 - - - -
5192 LEU* 4.2 16.8 - - + -
5562 VAL* 2.4 30.5 + - + +
5572 GLU 3.0 15.8 - - - +
5582 LYS 4.4 1.7 - - - +
5592 THR* 1.3 76.6 - - - +
5612 HIS* 1.3 65.2 + - - +
5622 ARG 3.4 25.0 - - - +
5632 ALA* 4.1 6.7 - - + -
6032 VAL* 5.1 6.5 - - + -
7642 MET* 5.8 0.2 - - - +
7672 ILE* 5.0 3.8 - - - -
7712 ARG* 5.7 3.4 - - - +
----------------------------------------------------------
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