Contacts of the strand formed by residues 1052 - 1057 (chain B) in PDB entry 1CM8
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 LYS1052 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043B SER* 5.1 8.9 + - - -
1044B ALA 3.4 10.5 - - - +
1045B VAL* 4.4 10.5 - - + +
1050B GLY 3.8 4.8 + - - +
1051B ALA* 1.3 76.1 - - - +
1053B VAL* 1.3 63.5 + - - +
1110B PRO* 4.4 1.6 - - - +
1111B PHE* 3.4 60.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1053 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027B TYR* 4.4 11.0 - - + -
1043B SER* 3.2 6.8 - - - -
1044B ALA* 2.9 32.8 + - + +
1046B ASP* 4.8 13.5 - - + +
1051B ALA* 4.1 10.3 - - + +
1052B LYS* 1.3 78.7 - - - +
1054B ALA* 1.3 67.3 + - - +
1055B ILE* 3.8 11.4 - - + -
1090B LEU* 3.7 29.6 - - + -
1108B VAL* 3.3 28.5 - - + -
1109B MET 4.0 1.1 - - - +
1110B PRO* 4.5 0.9 - - + -
1111B PHE* 3.6 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1054 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033B VAL* 6.2 0.4 - - + -
1041B VAL* 4.4 6.1 - - + -
1042B CYS 3.3 6.5 - - - +
1043B SER* 4.5 0.4 - - - +
1053B VAL* 1.3 73.3 - - - +
1055B ILE* 1.3 60.8 + - - +
1107B LEU 3.6 1.0 - - - +
1108B VAL* 3.4 4.5 - - - -
1109B MET* 2.5 44.4 + - + +
1110B PRO 4.1 0.9 - - - +
1111B PHE* 3.8 4.2 - - + +
1400B ANP 3.4 50.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1055 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021B TRP* 3.3 12.3 - - + -
1023B VAL* 4.3 8.3 - - + -
1027B TYR* 3.6 28.7 - - + -
1030B LEU* 3.8 9.9 - - + -
1041B VAL* 3.2 3.1 - - - -
1042B CYS* 2.5 43.6 + - + +
1044B ALA* 3.5 27.6 - - + -
1053B VAL* 3.8 13.5 - - + -
1054B ALA* 1.3 76.5 - - - +
1056B LYS* 1.3 60.3 + - - +
1093B PHE* 4.6 3.1 - - + -
1106B TYR* 3.9 31.6 - - + -
1107B LEU 3.4 7.9 - - - +
1108B VAL* 4.4 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1056 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021B TRP* 4.4 0.7 - - - -
1040B ALA 3.7 7.0 - - - +
1041B VAL* 3.7 16.4 - - + -
1054B ALA 4.1 0.4 - - - -
1055B ILE* 1.3 73.8 - - - +
1057B LYS* 1.3 68.9 + - - +
1058B LEU* 3.8 11.6 + - + +
1074B GLU* 2.8 33.8 + - - +
1106B TYR* 3.3 3.8 - - - -
1107B LEU* 2.8 56.6 + - + +
1109B MET* 4.7 12.1 - - + -
1171B ASP* 3.6 10.3 + - - +
1400B ANP 3.0 56.7 + - - +
1402B MG 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1057 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019B THR* 4.1 19.5 - - + -
1020B ALA 3.4 21.1 + - - +
1021B TRP* 3.7 26.9 - - + +
1040B ALA* 3.1 24.6 + - + +
1056B LYS* 1.3 75.6 - - - +
1058B LEU* 1.3 69.7 + - - +
1059B TYR* 3.0 16.2 + - - +
1060B ARG 5.8 1.0 - - - +
1104B ASP* 3.2 29.4 + - + +
1105B PHE 4.2 1.8 - - - +
1106B TYR* 3.5 44.7 + - + +
----------------------------------------------------------
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