Contacts of the strand formed by residues 512 - 514 (chain 5) 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 VAL 512 (chain 5).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2623 PRO* 3.4 19.3 - - + +
2633 GLU* 4.3 7.3 + - - +
4203 ARG* 4.3 13.2 - - - +
4233 LEU* 5.9 7.9 - - + -
4303 ILE* 6.3 0.7 - - + -
4313 ALA 4.5 6.7 - - - +
5015 THR* 3.5 35.0 - - + +
5025 ILE 3.5 12.6 - - - +
5035 SER* 3.6 27.4 - - - +
5105 THR 4.0 5.8 - - - +
5115 THR* 1.3 72.5 - - - +
5135 LEU* 1.3 58.4 + - - +
5145 ASN* 4.1 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 513 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2623 PRO* 4.3 9.9 - - + +
2703 LEU* 6.1 0.2 - - - -
2713 PRO* 4.8 13.9 - - + -
4515 ALA* 5.2 1.3 - - + -
4645 LEU* 3.5 40.6 - - + -
4705 VAL* 3.8 37.2 - - + -
5015 THR* 3.5 1.2 - - - -
5025 ILE* 2.9 44.8 + - + +
5045 ILE* 3.6 18.8 - - + -
5115 THR* 4.2 11.9 - - - +
5125 VAL* 1.3 73.8 - - - +
5145 ASN* 1.3 69.9 - - - +
5155 SER 3.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 514 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2623 PRO 3.9 5.3 + - - +
2633 GLU* 2.9 33.3 - - - +
2653 ALA* 4.6 3.5 - - + +
2683 GLY* 5.8 0.5 - - - -
4055 ARG* 3.5 17.2 - - - +
4705 VAL* 4.4 8.7 - - - +
4735 ASP* 3.5 18.1 - - - +
5005 GLN 3.7 4.0 + - - +
5015 THR* 3.5 21.2 - - - +
5125 VAL 4.9 0.4 + - - -
5135 LEU* 1.3 78.3 - - - +
5155 SER* 1.3 60.1 + - - +
5165 ARG* 2.5 46.2 + - + +
----------------------------------------------------------
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