Contacts of the strand formed by residues 31 - 36 (chain G) in PDB entry 2LNQ
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 ILE 31 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F LEU 3.9 4.3 - - - -
35F MET* 3.8 26.5 - - + +
36F VAL 4.8 2.2 - - - +
29G GLY* 4.1 9.9 - - - +
30G ALA* 1.3 83.6 - - - +
32G ILE* 1.3 68.0 + - - +
34H LEU* 3.7 0.7 - - - -
35H MET* 3.0 44.2 + - + +
38H GLY* 5.9 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 32 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F LEU* 3.7 30.5 - - + -
33F GLY* 3.8 0.3 - - - -
34F LEU* 2.7 41.7 + - + +
35F MET* 4.6 3.1 - - - +
19G PHE* 3.1 49.1 - - + -
21G ALA* 5.3 9.2 - - + -
30G ALA* 4.5 5.2 - - + -
31G ILE* 1.3 89.5 - - - +
33G GLY* 1.3 65.6 + - - +
34G LEU* 5.1 0.7 - - + -
32H ILE* 5.1 1.1 - - + -
33H GLY 3.6 6.3 - - - +
34H LEU* 3.1 31.4 - - + -
35H MET 4.4 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 33 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F ILE 3.9 7.4 - - - -
33F GLY* 4.0 5.4 - - - -
35F MET* 5.8 0.9 - - - -
32G ILE* 1.3 76.4 - - - +
34G LEU* 1.3 63.9 + - - +
32H ILE* 3.7 1.0 - - - +
33H GLY 3.0 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F PHE* 5.4 0.4 - - + -
21F ALA* 5.6 2.2 - - + -
31F ILE* 3.5 3.2 - - - +
32F ILE* 2.8 68.5 + - + +
34F LEU* 5.4 1.8 - - + -
17G LEU* 3.7 33.2 - - + -
19G PHE* 3.3 37.5 - - + -
33G GLY* 1.3 77.6 - - - +
35G MET* 1.3 65.7 + - - +
36G VAL* 5.1 5.6 - - + -
31H ILE 3.6 5.8 - - - +
32H ILE* 3.6 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 35 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F ALA 4.0 4.3 - - - -
31F ILE* 3.5 31.6 - - + +
34G LEU* 1.3 78.6 - - - +
36G VAL* 1.3 65.8 + - - +
37G GLY 4.9 11.2 - - - +
38G GLY* 5.6 5.2 - - - -
39G VAL 5.9 2.5 - - - +
30H ALA* 3.5 2.1 - - - +
31H ILE* 2.9 55.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F ASN* 5.1 5.2 - - - +
27F ASN* 3.8 17.0 - - - +
28F LYS* 4.9 0.7 - - - -
29F GLY* 3.7 11.9 + - - -
30F ALA* 2.8 43.9 + - + +
15G GLN* 4.7 21.8 - - + +
17G LEU* 4.2 23.8 - - + -
34G LEU* 5.1 4.5 - - + -
35G MET* 1.3 79.3 - - - +
37G GLY* 1.3 68.7 + - - +
29H GLY 3.4 0.2 - - - -
30H ALA* 3.9 17.5 - - + -
----------------------------------------------------------
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