Contacts of the strand formed by residues 405 - 411 (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 HIS 405 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3062 LEU* 4.4 3.4 - - - -
3892 THR* 6.0 6.7 - - + +
3902 LEU 3.6 12.3 - - - +
3912 GLN* 4.0 16.6 - - + +
4032 PRO 3.5 18.4 - - - +
4042 ARG* 1.3 76.2 - - - +
4062 ARG* 1.3 80.5 + - - +
4492 THR* 4.7 0.2 + - - -
2996 GLU* 3.4 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 406 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3062 LEU* 3.4 28.1 + - + +
3072 ARG 5.8 1.4 + - - -
3092 LEU* 3.2 44.0 + - + +
3202 VAL* 6.4 1.1 - - + -
3882 VAL 3.9 0.2 - - - +
3892 THR* 3.7 3.0 - - - -
3902 LEU* 2.9 42.6 + - + +
4052 HIS* 1.3 83.7 + - - +
4072 GLU* 1.3 66.2 + - - +
4082 VAL* 4.4 7.5 - - + +
4302 TYR* 3.7 14.5 - - - -
4492 THR* 3.1 49.6 + - - +
4512 ILE* 3.8 15.2 - - + +
2996 GLU* 3.6 10.5 + - - +
3006 VAL* 4.3 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 407 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3872 ARG* 3.1 36.6 + - + +
3882 VAL 3.8 10.1 - - - +
3892 THR* 4.3 21.3 - - + +
4062 ARG* 1.3 74.5 - - - +
4082 VAL* 1.3 65.0 + - - +
4092 ILE* 5.9 1.1 - - + +
4492 THR* 4.1 15.3 + - - +
4502 ILE* 3.5 22.7 - - + +
4512 ILE* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 408 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3872 ARG* 4.9 0.2 - - - -
3882 VAL* 2.9 47.8 + - + +
3902 LEU* 4.9 9.4 - - + -
4062 ARG* 4.4 13.0 - - + +
4072 GLU* 1.3 82.7 - - - +
4092 ILE* 1.3 75.1 + - - +
4102 LEU* 4.4 8.1 - - + -
4262 VAL* 4.4 27.1 - - + -
4512 ILE* 2.9 25.4 - - + +
4532 ALA* 4.2 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 409 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3562 ASN* 6.1 5.6 - - + -
3852 TYR* 3.4 40.8 - - + +
3862 GLN 3.8 3.4 - - - +
3872 ARG* 4.7 5.2 - - + +
4072 GLU* 5.9 2.0 - - + +
4082 VAL* 1.3 74.7 - - - +
4102 LEU* 1.3 69.2 + - - +
4112 LEU* 3.5 22.0 - - + -
4312 LYS* 4.8 11.7 - - + +
4502 ILE* 3.9 28.0 - - + -
4512 ILE 2.9 7.9 + - - -
4522 GLU* 3.5 20.0 - - + +
4532 ALA* 3.2 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 410 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3852 TYR* 3.6 1.4 - - - -
3862 GLN* 2.9 46.0 + - + +
3882 VAL* 3.6 27.4 - - + -
4082 VAL* 4.4 9.4 - - + +
4092 ILE* 1.3 80.2 - - - +
4112 LEU* 1.3 68.8 + - - +
4142 LEU* 3.6 23.6 - - + +
4152 VAL* 3.5 9.2 - - + +
4162 ASP* 3.6 16.4 - - - +
4172 VAL 5.0 0.4 - - - +
4182 SER* 4.4 14.6 - - - +
4522 GLU* 4.6 0.2 - - - -
4532 ALA* 4.6 2.9 - - + -
4562 ILE* 3.9 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 411 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2942 HIS* 4.1 4.2 + - + +
3332 GLN* 5.4 3.1 - - + -
3352 LYS* 3.2 37.0 - - - +
3832 ARG* 4.0 12.1 - - - +
3842 ASN 3.6 10.1 - - - +
3852 TYR* 4.7 6.1 - - + -
4092 ILE* 3.5 21.5 - - + -
4102 LEU* 1.3 81.1 - - - +
4122 ALA* 1.3 72.8 + - + +
4142 LEU* 3.1 27.2 + - + +
4152 VAL* 3.5 5.2 - - - -
4312 LYS* 6.0 0.9 - - - +
4522 GLU* 3.5 26.4 + - + +
----------------------------------------------------------
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