Contacts of the strand formed by residues 1171 - 1178 (chain A) in PDB entry 5DGY
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 VAL1171 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016A LYS* 3.6 47.1 - - + +
1017A VAL 3.8 8.5 - - - +
1018A SER* 3.9 11.2 - - - -
1023A VAL* 4.3 19.7 - - + +
1025A ILE* 4.3 19.9 - - + +
1150A VAL 4.3 0.3 - - - +
1151A LYS* 3.4 2.5 - - - +
1152A ALA* 2.9 51.7 + - + +
1169A SER 4.7 0.2 - - - +
1170A SER* 1.3 76.2 - - - +
1172A ARG* 1.3 64.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016A LYS* 2.8 39.8 + - - +
1025A ILE* 5.6 0.2 - - - -
1067A ARG* 6.0 0.2 - - - +
1149A GLU* 3.5 39.6 + - + +
1150A VAL 3.6 4.0 - - - -
1151A LYS* 3.7 33.8 - - + +
1165A ILE* 4.6 10.1 - - - +
1167A LYS* 6.2 0.6 - - - +
1170A SER* 4.4 13.7 + - - -
1171A VAL* 1.3 78.0 - - - +
1173A LEU* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014A PHE* 4.2 28.5 - - + +
1015A LYS* 5.0 7.0 - - - +
1016A LYS* 3.9 32.8 - - + +
1025A ILE* 4.7 15.0 - - + +
1027A LEU* 4.1 26.6 - - + +
1030A ARG* 3.3 32.5 - - + +
1149A GLU* 4.8 1.1 - - - -
1150A VAL* 2.9 37.0 + - - +
1172A ARG* 1.3 73.3 - - - +
1174A LEU* 1.3 67.7 + - - +
1175A ILE* 3.9 2.6 + - + +
1301A LYS* 5.9 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030A ARG* 3.1 37.2 + - - +
1147A ASP* 5.3 16.4 - - + +
1148A PHE 3.3 14.8 - - - +
1149A GLU* 4.3 7.7 - - + +
1172A ARG 4.4 0.4 - - - -
1173A LEU* 1.3 76.4 - - + +
1175A ILE* 1.3 68.6 + - - +
1176A ARG* 5.7 1.3 - - + -
1299A LYS 3.9 13.5 - - - +
1300A ILE* 3.5 37.8 - - + +
1301A LYS* 4.9 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027A LEU* 4.3 9.0 - - + -
1029A LYS 4.3 1.3 - - - +
1030A ARG* 3.3 25.6 - - + +
1032A TYR* 3.8 16.2 - - + -
1042A VAL* 3.6 22.9 - - + -
1062A LEU* 4.2 4.5 - - + -
1123A PHE* 3.8 16.6 - - + -
1130A SER* 4.5 2.4 + - - -
1147A ASP* 5.1 0.5 - - - +
1148A PHE* 3.0 41.1 + - + +
1150A VAL* 3.5 29.6 - - + -
1173A LEU* 4.2 7.2 - - + +
1174A LEU* 1.3 84.4 - - - +
1176A ARG* 1.4 69.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030A ARG 3.2 6.1 + - - +
1031A ASP* 2.9 35.5 + - - +
1032A TYR* 2.5 37.2 + - - +
1123A PHE* 5.6 0.8 - - - -
1130A SER* 3.9 17.3 - - - +
1148A PHE* 4.4 2.9 - - - -
1174A LEU* 5.7 1.8 - - + -
1175A ILE* 1.4 83.9 - - - +
1177A LYS* 1.3 54.8 + - - +
1178A VAL* 3.6 29.2 - - + +
1297A ASP* 4.9 8.8 - - - +
1298A GLY* 2.7 46.2 + - - +
1299A LYS* 4.8 1.2 - - - +
1300A ILE* 3.6 29.7 - - + +
1303A GLU* 5.5 1.6 + - - -
1305A THR* 4.9 5.1 + - - -
1358A HIS* 6.2 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032A TYR* 3.3 5.4 - - + +
1034A ASP* 2.9 43.8 + - + +
1039A VAL* 3.7 31.3 - - + +
1123A PHE* 4.4 14.8 - - + -
1124A PRO 4.5 1.5 + - - -
1125A ASP 5.9 1.2 + - - -
1127A LEU* 3.2 35.3 + - + +
1128A PRO 3.4 14.7 + - - +
1129A CYS* 3.3 25.7 - - - +
1130A SER* 4.0 4.0 - - - -
1148A PHE* 3.5 38.3 - - + -
1176A ARG* 1.3 71.5 - - - +
1178A VAL* 1.3 61.8 + - - +
1179A GLN* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1031A ASP* 4.9 8.1 - - + -
1032A TYR 3.0 11.0 + - - +
1033A VAL* 3.4 5.6 - - + +
1034A ASP 2.6 32.2 + - - -
1129A CYS* 5.2 1.6 - - - -
1130A SER* 5.5 2.5 - - - +
1176A ARG* 3.6 50.5 - - + +
1177A LYS* 1.3 74.1 - - - +
1179A GLN* 1.3 68.5 + - - +
1180A HIS* 4.1 18.5 + - + +
1297A ASP* 6.0 3.1 - - - +
1309A SER* 5.4 3.4 - - - +
1358A HIS* 4.8 15.3 - - + -
----------------------------------------------------------
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