Contacts of the helix formed by residues 640 - 648 (chain A) in PDB entry 2R5N
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 PRO 640 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A GLU* 3.6 23.8 - - - +
639A ALA* 1.4 89.3 - - + +
641A ALA* 1.3 66.8 + - - +
642A GLU* 3.7 23.8 - - - +
643A LEU* 3.0 33.1 + - + +
644A LEU* 3.1 9.4 + - - +
91B ARG 3.7 10.3 - - - +
92B GLN* 3.9 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 641 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ILE 4.0 4.9 - - - -
465A GLY* 3.2 38.8 - - - +
466A LEU 4.7 0.2 - - - -
467A GLY* 3.7 13.0 - - - -
468A GLU* 4.6 1.0 + - - -
521A GLN* 5.7 2.9 - - + -
639A ALA 3.4 2.4 + - - -
640A PRO* 1.3 72.4 - - - +
642A GLU* 1.3 62.7 + - - +
644A LEU* 3.0 4.6 + - - +
645A PHE* 2.9 39.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 642 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A PRO* 3.7 19.9 - - - +
641A ALA* 1.3 83.9 + - - +
643A LEU* 1.3 74.6 + - + +
645A PHE* 3.6 9.2 + - - +
646A GLU* 3.3 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 643 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A ALA* 4.8 4.3 - - + -
640A PRO* 3.0 32.0 + - + +
642A GLU* 1.3 89.7 - - + +
644A LEU* 1.3 62.5 + - - +
646A GLU* 3.4 20.7 + - - +
647A GLU* 2.8 29.2 + - - +
92B GLN* 5.3 3.1 - - - +
93B LEU* 4.7 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 644 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ILE* 3.4 32.3 - - + +
467A GLY* 4.0 2.0 - - - +
474A GLN* 3.2 29.8 - - - +
637A GLU* 3.4 31.9 - - + +
639A ALA* 3.4 31.9 - - + +
640A PRO 3.1 12.9 + - - +
641A ALA* 3.0 7.1 + - - +
643A LEU* 1.3 75.2 - - - +
645A PHE* 1.3 66.6 + - - +
647A GLU* 3.2 2.8 + - + -
648A PHE* 2.9 41.0 + - + +
93B LEU* 4.1 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 645 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A SER* 4.1 2.5 - - - -
464A ILE* 3.6 26.7 - - + -
465A GLY* 3.5 34.8 - - - -
521A GLN* 3.7 21.5 - - + -
560A GLU* 3.9 8.5 - - - -
613A ALA* 4.1 8.1 - - + -
641A ALA* 2.9 29.4 + - + +
642A GLU* 3.9 8.1 - - - +
644A LEU* 1.3 76.1 - - - +
646A GLU* 1.3 60.5 + - - +
648A PHE 3.5 0.5 + - - -
649A GLY 3.2 3.5 + - - -
650A PHE* 2.8 42.3 + + + +
680A EDO 3.5 46.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A GLU 3.3 11.2 + - - +
643A LEU* 3.5 26.0 - - - +
644A LEU 3.2 0.6 - - - -
645A PHE* 1.3 78.5 - - - +
647A GLU* 1.3 64.6 + - - +
649A GLY* 3.2 12.8 + - - -
651A THR* 3.8 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A GLU* 5.6 1.4 - - + +
643A LEU 2.8 20.5 + - - +
644A LEU* 3.5 8.5 - - - +
646A GLU* 1.3 75.7 - - - +
648A PHE* 1.3 81.3 + - + +
649A GLY 3.3 0.9 + - - -
93B LEU* 3.8 22.6 - - + +
94B HIS* 3.1 33.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 648 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ILE* 3.9 14.4 - - + -
630A VAL* 5.4 1.2 - - - +
631A GLY 4.4 7.4 - - - +
632A MET* 3.6 30.3 - - + -
633A THR 6.2 0.2 - - - -
634A THR* 3.3 23.3 - - + -
635A PHE 3.7 16.8 - - - -
636A GLY* 4.1 7.0 - - - -
637A GLU* 4.1 17.0 - - + -
644A LEU* 2.9 46.2 + - + +
647A GLU* 1.3 89.5 - - + +
649A GLY* 1.3 60.9 + - - +
650A PHE* 3.4 20.5 + - + -
----------------------------------------------------------
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