Contacts of the strand formed by residues 714 - 722 (chain B) in PDB entry 1L8A
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 TYR 714 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B TYR* 4.1 0.3 - - - -
664B TYR* 2.6 29.2 + + - -
665B GLU* 2.5 29.7 + - - -
702B PRO* 4.1 11.9 - - + -
705B ALA* 4.1 19.5 - - + +
708B GLY* 4.2 10.3 - - - -
709B ILE* 3.7 27.6 - - + -
713B ILE* 1.3 82.8 - - - +
715B LYS* 1.3 70.0 + - - +
716B LEU* 3.5 22.1 + - + +
756B TYR* 3.4 8.1 - - - -
757B SER* 3.1 45.9 + - - -
759B THR* 4.4 3.6 - - + -
791B VAL* 4.2 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 715 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B PRO* 5.4 3.1 - - - +
714B TYR* 1.3 79.9 - - - +
716B LEU* 1.3 66.2 + - - +
717B GLU* 4.1 13.0 - - - +
718B THR* 3.7 17.8 + - - +
754B ASP* 3.5 17.6 + - - +
755B VAL 3.6 11.4 - - - +
756B TYR* 3.4 38.4 + - + -
791B VAL* 4.2 12.2 + - + +
793B ASN* 4.2 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 716 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B TYR* 4.1 2.5 - - + -
664B TYR* 3.7 23.1 - - - +
699B PRO* 6.0 0.7 - - + -
702B PRO* 4.5 14.5 - - + +
714B TYR* 3.5 13.3 + - + +
715B LYS* 1.3 73.6 - - - +
717B GLU* 1.3 63.0 - - - +
735B LEU* 3.9 26.0 - - + -
739B ARG* 3.3 53.2 + - - +
755B VAL* 2.7 23.8 + - + +
757B SER* 4.1 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 717 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715B LYS* 3.5 6.5 - - - +
716B LEU* 1.3 85.4 - - - +
718B THR* 1.3 64.0 + - - +
719B ILE* 4.0 25.6 - - + +
739B ARG* 2.8 33.3 + - - +
743B GLU* 4.4 5.9 - - - +
754B ASP* 3.6 1.4 - - - -
755B VAL* 2.7 48.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 718 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715B LYS* 3.7 12.0 + - - +
717B GLU* 1.3 79.8 - - - +
719B ILE* 1.3 67.4 + - - +
720B GLU* 3.8 24.6 + - - +
725B LYS* 4.0 11.7 - - - +
753B SER 3.1 10.8 - - - +
754B ASP* 2.6 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 719 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717B GLU* 4.0 26.0 - - + +
718B THR* 1.3 80.7 - - - +
720B GLU* 1.3 66.7 + - - +
725B LYS* 4.9 0.9 + - - -
742B ALA* 4.0 18.8 - - + +
743B GLU* 3.2 34.1 - - - +
746B ALA* 3.6 29.2 - - + -
752B GLY* 3.1 3.1 - - - -
753B SER* 2.7 49.1 + - - +
755B VAL* 4.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 720 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718B THR* 3.8 22.1 + - - +
719B ILE* 1.3 88.5 - - - +
721B GLY* 1.3 59.7 + - - +
725B LYS* 5.5 2.1 + - - -
746B ALA* 4.2 8.1 - - - +
752B GLY* 3.7 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 721 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B GLU* 1.3 79.1 + - - +
722B SER* 1.3 60.4 + - - -
724B GLY 3.3 16.1 + - - +
725B LYS* 5.5 1.2 - - - +
750B GLY* 3.1 22.9 - - - -
752B GLY* 3.3 14.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 722 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721B GLY* 1.3 71.0 - - - -
723B LYS* 1.3 90.9 + - - +
724B GLY* 3.3 1.4 + - - -
750B GLY* 3.1 2.2 + - - -
----------------------------------------------------------
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