Contacts of the strand formed by residues 60 - 65 (chain W) 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 VAL 60 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68U TRP 5.8 3.6 - - - +
69U PHE* 4.8 20.6 - - + -
70U LEU 5.1 9.4 - - - +
71U ASP* 5.8 0.2 - - - +
72U HIS* 4.8 5.2 - - - -
7W MET* 5.1 3.6 - - + -
51W LEU 3.8 4.9 - - - +
52W ILE* 3.9 15.5 - - + -
59W GLU* 1.3 90.4 + - - +
61W LEU* 1.3 63.3 + - - +
62W THR* 3.5 28.7 - - - +
63W THR* 4.2 13.5 - - + +
92W VAL* 5.0 17.9 - - + +
96W ALA* 5.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72U HIS* 5.2 7.4 - - - -
73U ASP* 5.0 3.1 - - - +
51W LEU* 3.0 25.9 + - + +
52W ILE 4.4 2.9 - - - -
53W THR* 4.0 23.3 - - + +
59W GLU* 3.6 34.3 + - + +
60W VAL* 1.3 75.7 - - - +
62W THR* 1.4 67.9 + - - +
70W ARG* 5.6 7.4 + - - +
74W LYS* 3.9 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 62 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71U ASP* 5.6 0.4 - - - -
73U ASP* 3.8 17.9 - - - +
7W MET* 4.6 1.9 - - - +
50W GLY* 3.4 2.9 - - - -
51W LEU* 2.9 42.6 + - - +
60W VAL* 3.5 10.3 - - - +
61W LEU* 1.4 83.9 + - - +
63W THR* 1.3 74.1 + - - +
65W THR* 4.2 18.2 - - + -
70W ARG* 4.2 34.4 + - + +
71W ILE* 5.0 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 63 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69U PHE* 3.8 32.3 - - + -
71U ASP* 3.2 45.3 + - + +
73U ASP* 4.0 6.4 + - - +
7W MET* 5.5 2.7 - - + -
49W VAL 3.4 9.5 - - - +
50W GLY* 3.4 5.0 - - - -
60W VAL* 4.5 7.9 - - + -
62W THR* 1.3 92.3 - - - +
64W LEU* 1.3 72.7 + - + +
65W THR* 3.4 0.9 + - - +
96W ALA* 6.1 0.4 - - + -
101W GLN* 4.0 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69U PHE* 6.2 2.0 - - + -
5W SER* 3.9 32.1 - - - +
6W THR 4.1 1.6 - - - +
7W MET* 4.1 19.5 - - + -
48W ASN* 3.9 12.3 - - + -
49W VAL* 3.5 23.6 - - - +
50W GLY* 3.5 7.2 - - - +
63W THR* 1.3 82.5 + - + +
65W THR* 1.3 60.9 + - - +
96W ALA* 4.7 12.6 - - + +
97W LEU* 5.5 4.3 - - + +
99W HIS 4.7 0.2 - - - +
100W ARG* 4.4 23.8 - - + -
101W GLN* 3.6 24.5 - - + +
102W GLY* 3.8 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 65 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48W ASN* 3.5 4.7 + - - -
49W VAL* 3.0 41.8 + - + +
62W THR* 4.2 17.5 - - + -
63W THR 3.8 8.5 - - - +
64W LEU* 1.3 75.7 - - - +
66W PRO* 1.4 68.2 - - - +
67W ASP* 3.2 34.6 + - + +
70W ARG* 5.1 8.7 - - + -
71W ILE* 5.2 2.5 - - + -
----------------------------------------------------------
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