Contacts of the strand formed by residues 1048 - 1055 (chain A) in PDB entry 1YW2
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 HIS1048 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042A PHE* 3.1 11.0 - - - -
1043A ASP* 2.5 42.3 + - + -
1046A THR* 3.3 35.4 + - + +
1047A GLY* 1.3 83.3 + - - +
1049A ARG* 1.3 66.4 + - - +
1050A VAL* 4.7 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1049 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040A ALA* 5.9 1.6 - - - -
1041A ALA 3.1 13.2 - - - +
1042A PHE* 4.2 16.5 - - + -
1048A HIS* 1.3 80.0 + - - +
1050A VAL* 1.3 63.3 + - - +
1107A HIS* 4.3 2.8 - - - +
1108A LEU* 3.3 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1050 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1024A TYR* 3.8 28.0 - - + -
1040A ALA* 3.5 3.5 - - - -
1041A ALA 2.5 48.2 + - - +
1043A ASP* 4.1 20.0 - - + +
1048A HIS* 4.6 6.5 - - + +
1049A ARG* 1.3 78.6 - - - +
1051A ALA* 1.3 60.5 + - - +
1052A VAL* 4.0 11.8 + - + -
1087A LEU* 5.3 6.3 - - + -
1105A VAL* 3.9 15.3 - - + -
1106A THR 3.2 17.3 - - - +
1107A HIS* 4.8 2.2 - - - -
1108A LEU* 3.4 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1051 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038A VAL* 4.0 7.2 - - + -
1039A CYS 3.5 4.3 - - - -
1050A VAL* 1.3 76.2 - - - +
1052A VAL* 1.3 60.9 + - - +
1105A VAL* 3.5 5.5 - - - +
1106A THR 2.8 30.3 + - - +
1108A LEU* 3.6 16.2 - - + +
2001A PGJ 3.5 50.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1052 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018A TRP* 3.1 28.5 - - + -
1020A VAL* 4.5 3.8 - - + -
1024A TYR* 4.8 9.6 - - + -
1027A LEU* 4.4 7.0 - - + -
1038A VAL* 3.2 2.8 - - - -
1039A CYS 2.9 41.2 + - - +
1041A ALA* 4.3 12.8 - - + -
1050A VAL* 4.2 17.9 - - + -
1051A ALA* 1.3 76.8 - - - +
1053A LYS* 1.3 61.9 + - - +
1090A PHE* 4.2 16.2 - - + -
1103A TYR* 4.1 15.7 - - + -
1104A LEU 3.4 8.7 - - - +
1105A VAL* 4.6 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1053 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018A TRP* 4.2 1.6 - - - -
1035A TYR* 4.9 5.2 + - - +
1036A GLY* 5.3 2.7 - - - -
1037A SER 3.3 8.1 - - - +
1038A VAL* 4.0 12.6 - - + -
1052A VAL* 1.3 73.9 - - - +
1054A LYS* 1.3 66.0 + - - +
1055A LEU* 3.5 20.4 + - + -
1067A ARG* 4.7 3.0 - - - +
1071A GLU* 2.8 32.9 + - - +
1102A VAL 3.8 0.3 - - - +
1103A TYR* 3.4 4.9 - - - -
1104A LEU* 3.0 36.4 + - + +
1169A PHE* 3.3 12.1 + - - +
1170A GLY* 3.9 12.9 + - - -
2001A PGJ 2.9 58.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1054 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016A THR* 4.7 13.0 - - + +
1017A ILE* 3.0 25.1 + - - +
1018A TRP* 3.5 20.6 - - + -
1019A GLU* 3.3 2.2 + - - -
1036A GLY* 3.3 1.1 - - - -
1037A SER* 2.7 35.9 + - - +
1053A LYS* 1.3 72.1 - - - +
1055A LEU* 1.3 74.7 + - - +
1056A SER* 4.2 3.5 + - - -
1101A ASP* 3.0 37.0 + - - +
1102A VAL 3.8 4.9 - - - +
1103A TYR* 3.1 43.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1055 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035A TYR* 3.5 17.0 - - + +
1053A LYS* 3.5 29.3 + - - +
1054A LYS* 1.3 83.6 - - - +
1056A SER* 1.3 68.5 + - - +
1057A ARG 3.8 0.2 - - - -
1058A PRO* 4.0 18.0 - - + +
1067A ARG* 4.6 4.3 - - - +
1068A THR* 3.5 43.7 - - + +
1071A GLU* 3.9 13.9 - - + +
1101A ASP* 4.5 3.3 - - - +
1102A VAL* 3.1 33.4 + - + +
1104A LEU* 4.5 13.5 - - + -
----------------------------------------------------------
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