Contacts of the helix formed by residues 73 - 79 (chain Q) 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 73 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Q VAL* 5.5 7.6 - - + -
46Q LYS* 3.7 34.1 - - + +
69Q LEU* 3.2 17.4 + - + +
70Q LEU* 3.6 17.9 - - + +
72Q TYR* 1.4 83.4 - - + +
74Q ARG* 1.3 68.5 + - - +
75Q PRO 3.6 0.7 - - - -
76Q PHE* 3.2 27.0 + - - +
77Q LEU* 3.4 16.6 + - + +
88Q LEU* 5.5 5.2 - - + -
89Q VAL* 5.6 8.3 - - + -
92Q LEU* 6.0 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 74 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70Q LEU 4.3 5.2 - - - +
71Q LYS 3.3 13.8 + - - +
72Q TYR 3.2 0.8 - - - -
73Q VAL* 1.3 82.3 - - + +
75Q PRO* 1.3 73.1 - - + +
76Q PHE 3.2 0.5 + - - -
77Q LEU* 3.5 7.4 + - + +
78Q ASN* 3.1 50.0 + - - +
89Q VAL* 4.9 9.6 - - + -
116Q TRP* 3.3 84.3 + - + +
119Q SER* 4.0 12.7 + - - -
120Q GLU* 4.4 9.3 + - - +
122Q ARG* 5.7 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 75 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71Q LYS 3.8 5.6 - - - +
72Q TYR 3.7 12.8 - - - +
74Q ARG* 1.3 99.0 - - + +
76Q PHE* 1.3 65.6 + - + +
77Q LEU 3.5 0.4 + - - -
78Q ASN* 3.7 15.8 + - - +
79Q SER* 3.0 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 76 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Q ILE* 4.2 28.5 - - + -
36Q GLN 3.7 19.3 - - - -
37Q GLU* 5.3 2.0 - - - -
39Q ASP* 2.9 43.7 - - + +
42Q ALA* 4.7 2.2 - - + -
43Q VAL* 4.5 3.4 - - + +
46Q LYS* 3.8 29.2 - - + +
72Q TYR* 3.4 41.7 - + - -
73Q VAL* 3.2 11.9 - - - +
74Q ARG 3.1 0.4 - - - -
75Q PRO* 1.3 86.7 - - + +
77Q LEU* 1.4 60.7 + - + +
79Q SER* 3.0 13.3 + - - -
80Q ILE 4.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43Q VAL* 3.9 29.8 - - + -
46Q LYS* 3.6 33.2 - - + -
73Q VAL* 3.4 18.6 + - + +
74Q ARG* 4.0 6.5 - - + +
75Q PRO 3.5 0.2 - - - -
76Q PHE* 1.4 59.9 - - - +
78Q ASN* 1.3 62.2 + - - +
79Q SER 3.2 3.2 + - - -
80Q ILE* 3.6 10.7 + - - +
81Q SER 3.3 16.8 - - - +
84Q LYS* 3.9 28.3 - - + +
85Q ALA* 4.0 14.4 - - + +
88Q LEU* 3.9 28.0 - - + -
89Q VAL* 5.8 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 78 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74Q ARG* 3.1 56.0 + - - +
75Q PRO* 3.7 13.0 - - - +
76Q PHE 3.4 0.4 - - - -
77Q LEU* 1.3 73.6 - - - +
79Q SER* 1.3 63.8 + - - +
80Q ILE 3.4 0.9 + - - -
81Q SER* 3.8 12.2 + - - -
82Q LYS* 4.2 8.8 + - + +
85Q ALA* 3.6 22.8 - - - +
89Q VAL* 6.3 0.6 - - - +
120Q GLU* 5.5 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 79 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Q GLU 4.6 6.5 + - - -
38Q ASN 4.3 13.8 - - - +
39Q ASP* 3.4 13.3 + - - -
75Q PRO 3.0 19.1 + - - -
76Q PHE 3.0 14.1 + - - -
78Q ASN* 1.3 79.8 - - - +
80Q ILE* 1.3 58.1 + - - +
----------------------------------------------------------
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