Contacts of the strand formed by residues 649 - 653 (chain B) in PDB entry 1N1M
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 CYS 649 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624B ILE 4.2 0.6 + - - -
625B ALA* 3.5 24.1 - - - -
626B ILE* 3.3 23.3 + - - +
640B LEU* 3.9 9.0 - - - +
647B PHE* 4.1 2.1 - - - +
648B LYS* 1.3 75.9 - - - +
650B GLY* 1.3 59.4 + - - +
699B GLU* 3.1 23.6 - - + +
758B PHE* 3.8 15.5 - - + -
759B ILE* 4.5 4.7 - - - -
762B CYS* 2.0 48.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 650 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625B ALA* 5.3 0.7 - - - -
626B ILE 2.9 15.5 - - - -
640B LEU* 3.7 19.2 - - - +
649B CYS* 1.3 80.1 - - - +
651B ILE* 1.3 66.4 + - - +
699B GLU 3.1 4.9 + - - +
700B TYR* 3.7 6.4 - - - -
701B LEU 3.2 22.7 + - - -
758B PHE* 3.8 2.6 - - - -
759B ILE* 6.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 651 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B TRP* 4.4 2.0 - - + -
626B ILE 3.0 6.3 + - - -
627B TRP* 3.1 27.3 - - + -
628B GLY 3.2 7.0 + - - +
636B THR* 3.4 6.0 - - - +
650B GLY* 1.3 78.0 - - - +
652B ALA* 1.3 63.4 + - - +
653B VAL* 4.3 4.5 - - + -
701B LEU* 3.5 23.8 - - + +
703B ILE* 4.1 8.3 - - + -
755B MET* 3.4 56.8 - - + +
758B PHE* 3.6 28.9 - - + -
759B ILE* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 652 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B GLY 3.7 4.3 - - - -
633B GLY* 3.8 14.1 - - - +
636B THR* 4.6 1.8 - - + -
637B SER* 3.6 23.6 - - - +
650B GLY 4.4 0.2 + - - -
651B ILE* 1.3 74.1 - - - +
653B VAL* 1.3 63.2 + - - +
655B PRO* 3.8 9.9 - - + +
700B TYR* 3.8 19.3 - - + +
701B LEU 3.1 7.7 + - - +
702B LEU* 3.9 0.8 - - - -
703B ILE 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 653 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627B TRP* 3.9 27.4 - - + -
628B GLY 3.0 6.7 + - - +
629B TRP* 3.3 44.8 - - + -
630B SER 2.9 23.2 + - - -
633B GLY* 4.2 0.5 - - - -
651B ILE* 4.3 3.6 - - + -
652B ALA* 1.3 73.1 - - - +
654B ALA* 1.3 68.7 + - - +
655B PRO* 3.3 2.8 - - - +
703B ILE* 3.5 8.5 - - + +
742B ILE* 3.8 16.8 - - + -
751B ILE* 3.8 10.1 - - + -
755B MET* 4.0 20.0 - - + -
----------------------------------------------------------
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