Contacts of the strand formed by residues 6119 - 6122 (chain P) in PDB entry 1LD4
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 ALA6119 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6047P ILE* 3.0 21.1 - - - +
6048P THR* 3.1 31.3 + - - +
6049P CYS* 5.3 0.7 - - - -
6118P HIS* 1.3 80.6 - - - +
6120P GLN* 1.3 63.4 + - - +
6121P ALA 3.8 0.5 + - - -
6178P VAL* 4.2 10.8 - - + -
6179P ILE 3.4 13.9 - - - +
6180P HIS* 4.2 15.0 - - + -
6189P PHE* 5.7 2.2 - - + -
6240P PHE* 6.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN6120 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6044P GLN* 5.5 10.3 - - + +
6046P TYR 3.8 4.3 - - - +
6047P ILE* 3.9 24.1 - - + +
6118P HIS* 5.5 3.7 - - + +
6119P ALA* 1.3 75.3 - - - +
6121P ALA* 1.3 64.3 + - - +
6122P ILE* 3.6 13.9 + - + +
6178P VAL* 3.2 8.6 - - - -
6179P ILE* 3.2 58.7 + - + +
6208P LEU* 4.7 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA6121 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6044P GLN* 4.4 0.5 - - - -
6045P GLU* 3.6 16.3 + - - -
6046P TYR* 2.7 41.0 + - + +
6047P ILE* 5.2 0.7 - - - -
6048P THR* 6.1 0.4 - - - +
6119P ALA 3.8 2.4 + - - -
6120P GLN* 1.3 69.9 - - - +
6122P ILE* 1.3 65.6 + - - +
6178P VAL* 3.8 17.9 - - + +
6189P PHE* 4.3 21.1 - - + -
6192P TYR* 4.4 9.8 + - + +
6204P GLN* 4.7 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE6122 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6042P THR* 3.7 25.4 - - + -
6043P ASN 3.6 32.8 - - - +
6044P GLN* 4.5 11.7 - - + -
6045P GLU* 6.0 0.2 - - - -
6120P GLN* 3.8 13.5 - - + +
6121P ALA* 1.3 81.0 - - - +
6123P LYS* 1.3 81.3 + - - +
6124P VAL* 3.9 8.7 - - + +
6176P LYS* 3.5 8.3 - - - +
6177P VAL 3.2 34.5 + - - +
6178P VAL* 4.5 1.3 - - - +
6179P ILE* 4.2 15.0 - - + -
6192P TYR* 5.0 3.1 + - - -
6266P LEU* 3.7 22.4 - - + -
----------------------------------------------------------
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