Contacts of the strand formed by residues 670 - 674 (chain B) in PDB entry 1RL3
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 GLU 670 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B VAL* 4.2 11.4 - - + -
537B SER* 6.0 0.7 - - - +
668B ALA 3.4 0.6 + - - -
669B LEU* 1.3 73.6 - - - +
671B PRO* 1.3 72.7 - - + +
672B VAL* 3.3 9.0 + - + +
746B VAL* 3.1 4.3 - - - -
747B LYS* 2.9 69.9 + - + +
748B LEU 6.0 0.2 - - - -
752B ARG* 3.5 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 671 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B VAL* 5.5 1.6 - - + -
538B HIS* 5.5 8.7 - - + +
640B LYS* 4.7 9.4 - - + +
644B TYR* 3.7 22.4 - - + +
669B LEU 3.3 10.5 - - - +
670B GLU* 1.3 88.1 - - + +
672B VAL* 1.3 65.9 + - - +
673B GLN* 3.9 13.0 + - - +
694B LEU* 6.0 1.3 - - + -
745B CYS 3.5 7.2 - - - +
746B VAL* 4.1 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 672 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B GLU* 3.7 19.5 - - - +
671B PRO* 1.3 79.1 - - - +
673B GLN* 1.3 62.4 + - - +
674B PHE* 4.1 18.1 - - + -
691B PHE* 5.2 0.9 - - + -
743B LEU 4.0 0.5 - - - +
745B CYS* 2.7 63.5 + - + +
747B LYS* 3.8 41.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 673 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B PRO* 3.9 14.1 + - - +
672B VAL* 1.3 86.9 - - - +
674B PHE* 1.3 75.8 + - - +
678B GLN* 4.2 1.6 + - - -
743B LEU 3.2 9.0 - - - +
744B LYS* 2.9 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 674 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672B VAL* 4.1 22.0 - - + -
673B GLN* 1.3 82.8 - - - +
675B GLU* 1.3 64.5 + - - +
678B GLN* 3.0 30.5 - - + +
679B LYS 5.6 0.2 - - - -
680B ILE* 3.5 51.1 - - + -
691B PHE* 4.3 15.7 - + - -
739B ALA* 4.5 0.2 - - + -
742B PRO* 3.8 6.2 - - - +
743B LEU* 2.6 44.3 + - + +
745B CYS* 4.1 20.4 - - + -
747B LYS* 6.3 0.2 - - + -
----------------------------------------------------------
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