Contacts of the strand formed by residues 52 - 59 (chain 3) in PDB entry 4C2M
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 GLN 52 (chain 3).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792 GLY 3.6 0.3 - - - +
802 LEU* 3.6 2.8 - - - -
812 PHE* 2.8 66.4 + - + +
832 PRO* 5.0 4.0 - - - +
503 GLN 4.5 7.0 - - - +
513 GLN* 1.3 81.6 - - - +
533 VAL* 1.3 64.5 + - - +
543 TRP* 3.9 19.1 + - - +
1343 ASP* 3.6 31.2 + - - +
1353 LYS* 4.5 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782 VAL* 3.8 22.4 - - + -
792 GLY 3.3 7.9 - - - +
802 LEU* 3.8 19.7 - - + -
403 LEU* 4.1 10.8 - - + -
513 GLN* 4.8 4.3 - - + +
523 GLN* 1.3 75.4 - - - +
543 TRP* 1.3 65.3 + - - +
1093 LEU* 4.0 17.5 - - + -
1313 LEU* 3.6 28.3 - - + -
1323 GLN 5.3 0.2 - - - +
1333 PHE* 3.7 10.5 - - + -
1343 ASP* 2.8 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 54 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102 ILE* 5.4 4.7 - - + -
782 VAL* 3.3 9.7 - - - +
792 GLY* 2.7 45.0 + - - +
812 PHE* 3.8 39.0 - + + -
882 ILE* 3.6 27.8 - - + -
523 GLN* 3.9 25.4 - - + +
533 VAL* 1.3 82.0 - - - +
553 LEU* 1.3 59.8 + - - +
563 ILE* 4.2 13.5 - - + -
703 LEU* 4.8 11.0 - - + -
713 PRO 5.5 5.2 - - - -
723 VAL* 5.0 15.0 - - + -
1333 PHE* 3.7 4.0 - - - -
1343 ASP* 4.3 0.2 - - + -
1353 LYS* 3.3 37.5 - - + +
1373 PHE* 3.8 33.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232 VAL* 4.4 7.9 - - + -
762 TYR* 4.2 28.7 - - + -
772 VAL 3.7 13.2 - - - +
782 VAL* 4.2 11.7 - - + -
932 ALA* 5.8 0.4 - - + -
952 VAL* 5.0 2.9 - - + -
543 TRP* 1.3 73.5 - - - +
563 ILE* 1.3 64.5 + - - +
1073 MET* 3.5 38.1 - - + -
1333 PHE* 3.7 30.6 - - + -
1353 LYS 3.0 6.9 + - - +
1363 VAL* 3.2 21.7 - - + +
1373 PHE 2.7 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752 GLN 3.9 0.5 - - - +
762 TYR* 3.6 6.3 - - - -
772 VAL* 2.8 45.9 + - + +
792 GLY* 5.3 1.6 - - - -
882 ILE* 4.4 3.1 - - + -
902 LEU* 4.4 22.2 - - + -
543 TRP* 4.2 28.9 - - + -
553 LEU* 1.3 81.6 - - - +
573 LYS* 1.3 66.7 + - - +
583 PHE* 3.5 31.7 + - + -
703 LEU* 4.5 12.8 - - + -
893 ILE* 6.0 0.9 - - + -
1373 PHE* 3.3 22.0 - - + +
1393 VAL* 4.3 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732 SER 4.2 2.8 + - - -
742 ASN* 3.1 45.5 + - - +
752 GLN 3.4 5.2 - - - +
762 TYR* 3.4 24.3 - - + +
553 LEU 4.4 0.2 - - - -
563 ILE* 1.3 71.9 - - - +
583 PHE* 1.3 74.4 - - - +
593 PRO* 4.1 8.7 - - - +
1373 PHE 2.8 14.7 + - - +
1383 SER* 3.4 21.3 - - - +
1393 VAL* 2.8 47.0 + - - +
1403 SER* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 58 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742 ASN 3.6 0.5 - - - -
752 GLN* 2.6 39.2 + - + +
772 VAL* 4.4 10.8 - - + -
902 LEU* 5.0 4.9 - - + -
563 ILE* 3.5 36.8 - - + -
573 LYS* 1.3 81.6 - - - +
593 PRO* 1.3 71.4 - - + +
623 VAL* 4.5 11.0 - - + -
643 ILE* 4.0 33.4 - - + -
673 LEU* 4.1 21.3 - - + -
703 LEU* 4.7 14.8 - - + -
823 ILE* 3.8 25.1 - - + -
1393 VAL* 4.0 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 59 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732 SER 3.6 10.8 - - - +
752 GLN* 3.6 4.9 - - - +
573 LYS* 4.3 7.4 - - - +
583 PHE* 1.3 86.5 - - + +
603 SER* 1.3 66.0 + - - +
613 ASN* 3.6 24.0 - - - +
623 VAL* 3.0 26.3 + - + +
873 TYR* 3.7 26.7 - - + -
1393 VAL* 3.3 26.9 - - + +
1403 SER* 4.9 1.8 - - - -
1413 GLU* 5.0 4.7 - - + +
----------------------------------------------------------
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