Contacts of the strand formed by residues 1057 - 1068 (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 LYS1057 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1056A LYS* 1.3 73.6 - - - +
1058A VAL* 1.3 64.8 + - - +
1059A TYR* 3.4 41.7 - - + +
1090A GLN* 2.9 44.8 + - - +
1092A TYR 3.5 12.1 - - - +
1093A PRO* 2.5 41.6 + - + +
1154A ALA* 3.8 0.9 - - - -
1155A SER* 2.8 35.4 + - - +
1156A ASP 5.4 1.8 - - - +
1157A ILE 4.6 6.3 - - - +
1158A THR* 6.1 0.4 - - - -
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Residues in contact with VAL1058 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023A VAL* 4.6 17.7 - - + -
1046A VAL* 5.3 3.6 - - + -
1048A VAL* 4.3 17.0 - - + -
1053A VAL* 3.7 30.1 - - + -
1057A LYS* 1.3 75.5 - - - +
1059A TYR* 1.3 70.9 + - - +
1090A GLN* 3.8 0.7 - - - -
1091A VAL* 3.0 32.6 + - + -
1092A TYR* 3.2 30.6 + - + +
1152A ALA* 5.5 1.3 - - + -
1153A PHE 3.4 15.7 - - - +
1154A ALA* 4.2 9.9 - - + -
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Residues in contact with TYR1059 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057A LYS* 3.4 39.7 - - + +
1058A VAL* 1.3 75.7 - - - +
1060A VAL* 1.4 60.6 + - - +
1061A THR* 4.1 5.1 + - + -
1088A ARG* 5.2 5.4 - - + -
1089A VAL 3.4 10.1 - - - +
1090A GLN* 3.6 33.0 - - + -
1091A VAL* 4.3 1.3 - - - -
1151A LYS 4.2 0.3 - - - +
1152A ALA* 3.5 3.6 - - - +
1153A PHE* 3.0 63.6 + + + +
1155A SER* 5.1 3.8 - - - -
1157A ILE 4.0 10.1 - - - -
1158A THR* 3.4 8.2 - - - -
1159A ASP* 3.1 50.3 + - - +
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Residues in contact with VAL1060 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025A ILE* 4.5 4.3 - - + -
1046A VAL* 4.8 1.8 - - + -
1059A TYR* 1.4 72.9 - - - +
1061A THR* 1.3 56.6 + - - +
1089A VAL* 2.4 60.4 + - + +
1090A GLN 4.1 2.9 - - - +
1091A VAL* 3.4 28.1 - - + +
1119A PHE* 3.5 57.4 - - + -
1121A LEU* 4.1 7.6 - - + -
1150A VAL* 4.6 2.2 - - + -
1151A LYS 3.8 6.5 - - - +
1152A ALA* 4.4 13.5 - - + +
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Residues in contact with THR1061 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059A TYR* 4.3 4.3 - - + -
1060A VAL* 1.3 81.1 - - - +
1062A LEU* 1.4 62.5 + - - +
1063A THR* 4.1 5.7 + - - -
1086A PHE* 4.3 13.6 - - + -
1087A SER 3.8 2.7 - - - -
1088A ARG* 3.7 23.8 - - + -
1121A LEU* 4.0 3.6 - - - -
1149A GLU 3.9 0.9 - - - +
1150A VAL* 3.6 5.7 - - - +
1151A LYS* 2.7 54.2 + - - +
1153A PHE* 3.3 35.2 - - + -
1162A GLU* 5.2 0.9 - - + -
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Residues in contact with LEU1062 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1042A VAL* 4.2 4.0 - - + -
1061A THR* 1.4 74.8 - - - +
1063A THR* 1.4 68.3 + - - +
1064A CYS* 4.3 1.3 - - + +
1085A TYR* 5.2 7.2 - - + -
1086A PHE* 3.5 1.2 - - - -
1087A SER* 2.5 64.0 + - - +
1121A LEU* 3.7 30.4 - - + +
1122A THR 3.7 24.5 - - - +
1123A PHE* 3.8 35.2 - - + -
1148A PHE* 5.5 2.2 - - + -
1149A GLU 4.5 3.1 - - - +
1150A VAL* 3.9 25.8 - - + -
1175A ILE* 4.2 5.6 - - + -
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Residues in contact with THR1063 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061A THR* 4.1 7.8 + - - -
1062A LEU* 1.4 80.7 - - - +
1064A CYS* 1.4 71.6 + - - +
1065A ALA* 3.9 8.4 + - + -
1081A ARG* 6.0 2.5 - - - +
1083A ASP* 4.0 20.6 - - - +
1085A TYR 3.9 2.5 - - - +
1086A PHE* 3.3 24.7 - - + -
1148A PHE* 3.8 2.1 - - - +
1149A GLU* 3.0 53.7 + - + +
1151A LYS* 5.5 4.4 - - - +
1162A GLU* 5.2 0.9 + - - +
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Residues in contact with CYS1064 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062A LEU* 4.3 1.6 - - + +
1063A THR* 1.4 72.0 - - - +
1065A ALA* 1.4 60.5 - - - +
1083A ASP* 3.7 5.9 - - - +
1084A LEU* 3.2 32.5 + - - -
1085A TYR* 2.3 67.8 + - + +
1127A LEU* 4.4 8.3 - - + -
1128A PRO* 4.8 3.4 - - - -
1146A VAL* 4.5 5.6 - - - -
1147A ASP 4.4 0.7 - - - -
1148A PHE* 3.4 42.8 - - + -
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Residues in contact with ALA1065 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063A THR* 3.9 10.0 + - + +
1064A CYS* 1.4 73.9 - - - +
1066A PHE* 1.3 59.5 + - - +
1067A ARG* 4.0 16.8 - - - +
1081A ARG* 4.7 11.0 - - - +
1083A ASP* 4.1 20.9 - - - +
1084A LEU* 4.6 2.0 - - - -
1146A VAL* 3.7 5.8 - - - +
1147A ASP* 3.1 48.4 + - - +
1149A GLU* 6.2 1.3 - - + -
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Residues in contact with PHE1066 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A PRO* 4.1 4.5 - - + -
1065A ALA* 1.3 72.3 - - - +
1067A ARG* 1.3 78.1 + - - +
1068A TYR* 4.0 2.2 - + - -
1081A ARG* 3.6 17.3 - - - +
1082A ARG* 3.0 28.8 + - + +
1084A LEU* 3.9 21.8 - - + +
1144A CYS* 3.9 15.3 - - - -
1145A GLY 4.4 1.8 - - - -
1146A VAL* 3.5 17.0 - - + +
1248A VAL* 4.2 12.6 - - + -
1249A VAL 4.3 6.1 - - - -
1250A LEU* 3.6 34.5 - - + -
1323A GLY* 3.8 22.0 - - - -
1324A ILE* 3.7 35.9 - - + -
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Residues in contact with ARG1067 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065A ALA* 4.5 11.6 - - - +
1066A PHE* 1.3 79.0 - - - +
1068A TYR* 1.3 60.2 + - - +
1069A GLY 5.9 1.1 - - - +
1071A GLU* 5.0 14.5 + - - +
1081A ARG* 3.1 48.3 - - - +
1143A SER 4.9 1.1 - - - +
1144A CYS* 3.3 7.8 - - - -
1145A GLY 3.0 40.5 + - - +
1147A ASP* 2.9 39.0 + - - +
1149A GLU* 2.8 31.7 + - - +
1172A ARG* 6.0 0.2 - - - +
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Residues in contact with TYR1068 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A VAL* 4.6 8.3 - - + -
139A VAL* 4.3 21.0 - - + +
142A PRO* 4.3 4.9 - - + -
145A ASN* 3.2 33.9 - - - +
1066A PHE* 4.0 3.8 - + - -
1067A ARG* 1.3 77.8 - - - +
1069A GLY* 1.3 65.8 + - - +
1070A GLN 4.4 1.2 - - - +
1074A ASP* 3.8 36.8 + - - +
1079A THR* 4.8 1.6 + - - +
1080A PHE 3.6 16.8 + - - -
1081A ARG* 3.8 20.1 - - - +
1082A ARG 4.0 6.7 + - - -
1143A SER 3.9 2.0 - - - -
1144A CYS* 3.6 20.6 - - - -
1250A LEU* 3.8 32.5 - - + -
1251A TYR* 3.9 15.0 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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