Contacts of the strand formed by residues 54 - 60 (chain 2) in PDB entry 5LN3
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 GLY 54 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502 VAL* 3.7 0.7 - - - +
512 TYR* 2.8 42.9 + - - +
522 LYS 3.6 0.2 - - - -
532 ASP* 1.4 80.3 - - - +
552 ILE* 1.4 65.1 + - - +
1462 VAL* 4.6 4.0 - - - -
1512 PRO* 4.8 1.6 - - - +
2212 ILE 3.5 11.4 - - - -
2222 SER* 4.2 2.9 - - - -
2232 LYS* 3.8 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 55 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492 VAL 3.7 7.9 - - - +
502 VAL* 3.7 19.1 - - + -
512 TYR* 3.6 1.9 - - - -
542 GLY* 1.4 76.6 - - - +
562 VAL* 1.3 80.0 + - - +
572 LEU* 4.4 12.8 - - + -
1442 GLY* 5.8 0.7 - - - -
1452 GLY 3.6 19.7 - - - +
1462 VAL* 4.7 2.0 - - + -
1512 PRO* 3.9 13.0 - - + -
1522 HIS 3.4 28.0 - - - +
1532 LEU* 4.4 15.7 - - + -
2202 VAL* 3.6 3.8 - - - +
2212 ILE* 2.8 51.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482 GLY* 3.4 1.2 - - - -
492 VAL 3.0 31.5 + - - +
512 TYR* 3.6 25.6 - - + -
552 ILE* 1.3 82.6 - - - +
572 LEU* 1.4 70.8 + - - +
1912 GLU* 4.7 3.4 - - - +
1942 ALA* 3.8 20.2 - - + -
1952 LYS* 4.6 8.7 - - + +
1982 VAL* 4.1 28.9 - - + -
2182 LEU* 4.4 10.3 - - + -
2192 CYS 3.5 7.6 - - - +
2202 VAL* 4.0 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472 ALA 3.4 15.5 - - - +
482 GLY* 4.4 3.1 - - - -
552 ILE* 4.4 13.7 - - + -
562 VAL* 1.4 85.6 - - - +
582 GLY* 1.3 59.5 + - - +
772 ILE* 4.2 24.2 - - + -
852 TYR* 4.2 19.3 - - + +
862 CYS* 5.7 0.2 - - - -
872 CYS* 4.6 17.0 - - - +
1422 VAL* 4.4 23.3 - - + +
1442 GLY* 5.3 6.3 - - - +
1532 LEU* 4.6 4.3 - - + -
1982 VAL* 4.6 1.1 - - - -
2182 LEU* 3.7 0.7 - - - -
2192 CYS* 2.8 40.3 + - + +
2212 ILE* 4.9 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 58 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462 ILE* 3.5 0.7 - - - +
472 ALA 2.8 31.2 + - - +
572 LEU* 1.3 76.4 - - - +
592 ALA* 1.4 64.6 + - - +
872 CYS* 5.3 2.3 - - - -
1982 VAL* 4.1 18.8 - - - +
2022 ILE* 4.1 6.3 - - - -
2172 ASP 3.5 11.9 - - - -
2182 LEU* 4.1 2.2 - - - -
2192 CYS 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452 THR 3.1 12.3 - - - +
462 ILE* 3.7 18.2 - - + -
582 GLY* 1.4 76.3 - - - +
602 ASP* 1.4 64.8 + - - +
612 THR* 3.9 0.4 + - - +
762 LYS* 5.6 7.4 - - + +
772 ILE* 6.1 0.7 - - + +
872 CYS* 4.6 12.1 - - - -
2022 ILE* 4.1 10.4 - - - +
2162 ILE* 4.0 2.1 - - - +
2172 ASP* 3.0 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 60 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442 THR* 3.3 36.4 + - - +
452 THR* 2.8 23.3 + - - +
592 ALA* 1.4 79.2 - - - +
612 THR* 1.4 57.8 + - - +
622 ARG* 4.2 4.5 - - - +
762 LYS* 5.8 1.9 - - - +
2022 ILE* 3.7 15.5 - - + -
2062 ILE* 3.4 25.7 - - - +
2122 SER* 3.4 24.7 - - - -
2132 GLY 3.0 23.8 + - - +
2152 ASN 3.5 6.4 - - - +
----------------------------------------------------------
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