Contacts of the strand formed by residues 362 - 369 (chain A) in PDB entry 5IYB
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 SER 362 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A VAL* 3.2 32.2 + - - +
360A ASP 3.7 1.0 + - - -
361A PHE* 1.3 81.3 + - - +
363A ALA* 1.3 63.7 + - - +
388A MET* 3.6 5.4 - - - +
503A LEU 3.3 8.3 - - - -
504A HIS* 4.3 2.5 + - - -
1061B SER* 3.2 3.9 - - - -
1062B ARG* 3.0 33.1 + - - +
1084B LEU* 3.5 33.4 - - - -
1106B ARG* 4.0 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A SER* 1.3 76.9 - - - +
364A ARG* 1.3 60.5 + - - +
384A ILE* 3.5 31.9 - - + -
388A MET* 4.5 3.1 - - - -
482A PHE* 3.9 13.2 - - + -
503A LEU* 2.6 45.6 + - + -
1060B HIS 3.4 9.4 - - - +
1061B SER* 4.1 1.8 - - - +
1084B LEU* 3.3 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ALA* 1.3 76.8 - - - +
365A THR* 1.3 66.2 + - - +
384A ILE* 4.5 0.4 - - - +
461A GLN* 4.1 4.9 - - - +
482A PHE* 3.8 1.8 - - - -
500A GLU* 2.4 51.7 + - + +
501A MET 3.4 5.6 - - - +
502A ASN* 3.4 16.4 + - - +
1058B LYS* 4.1 18.6 + - + +
1059B ILE* 3.8 1.7 - - - +
1060B HIS* 3.0 37.8 + - + +
1084B LEU* 3.6 26.3 - - + +
53Y G 4.2 13.5 + - - -
54Y A 3.6 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ARG* 1.3 75.7 - - - +
366A VAL* 1.3 67.8 + - - +
384A ILE* 4.2 5.2 - - + -
480A SER 2.8 22.3 + - - +
481A THR* 3.7 3.5 - - - -
482A PHE* 3.2 57.9 - - + +
500A GLU* 3.5 6.9 - - - -
501A MET 3.1 26.1 + - - -
1055B VAL* 4.2 4.0 - - - +
1058B LYS* 4.8 6.3 - - - -
1059B ILE* 3.9 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A THR* 1.3 80.2 + - - +
367A ILE* 1.3 73.0 + - - +
481A THR* 3.0 21.6 - - + -
482A PHE 3.0 24.1 + - - -
498A GLY* 4.2 11.7 - - - +
499A ASP 3.8 10.8 - - - +
500A GLU* 4.7 0.9 - - - +
932B GLY 4.2 7.9 - - - +
944B THR* 4.1 22.7 - - + +
1053B HIS 6.0 1.3 - - - +
1055B VAL* 4.0 17.7 - - + -
1058B LYS* 4.0 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A VAL* 1.3 84.5 - - - +
368A THR* 1.3 67.4 + - - +
481A THR* 4.4 0.2 - - - -
482A PHE* 3.4 14.8 - - + +
484A LEU* 3.4 22.7 - - + -
494A ALA* 3.6 31.0 - - + -
496A PHE* 3.3 34.1 - - + +
498A GLY 5.3 0.2 + - - -
499A ASP* 3.0 29.2 - - + +
501A MET* 3.4 33.2 - - + -
944B THR* 4.2 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ILE* 1.3 80.3 - - - +
369A PRO* 1.3 74.7 - - + +
481A THR* 3.3 14.0 + - + +
482A PHE 3.5 4.4 + - - -
483A ARG* 2.5 47.8 + - - +
484A LEU 3.6 1.7 + - - -
496A PHE* 3.3 10.8 - - - -
931B ILE* 3.6 10.5 - - + -
932B GLY 4.4 0.7 - - - +
944B THR* 3.7 16.4 - - + -
945B CYS 3.6 23.8 - - - +
946B GLY* 4.1 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A THR* 1.3 88.3 - - - +
370A ASP* 1.3 59.3 + - - +
371A PRO* 4.2 3.8 - - + -
483A ARG* 3.7 5.4 + - - -
484A LEU 4.0 0.9 - - - +
486A LEU* 3.2 31.2 - - + -
496A PHE* 3.6 20.1 - - + -
788B TYR* 3.1 51.8 - - - +
790B GLN* 3.5 20.4 - - + +
793B SER* 3.8 15.0 - - - +
946B GLY* 4.4 1.3 - - - +
----------------------------------------------------------
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