Contacts of the strand formed by residues 1088 - 1097 (chain A) in PDB entry 1Y1S
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 THR1088 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1020A GLN 3.0 7.8 + - - -
1021A LEU* 3.3 27.4 - - + +
1022A ALA 2.7 32.3 + - - +
1086A ILE* 3.5 3.8 - - - +
1087A ARG* 1.3 83.3 - - - +
1089A PHE* 1.3 63.9 + - - +
1090A LEU* 4.9 0.2 - - + -
1136A CYS* 3.6 30.3 - - - -
1212A ARG* 3.0 37.0 + - - +
1252A LEU* 4.3 3.5 + - + -
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Residues in contact with PHE1089 (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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1022A ALA* 3.3 13.5 - - + +
1024A VAL* 4.2 15.0 - - + -
1078A VAL* 3.7 35.4 - - + -
1081A LEU* 3.8 20.9 - - + -
1082A ALA* 4.3 3.6 - - + -
1086A ILE* 3.3 38.1 - - + -
1087A ARG 4.2 3.6 - - - -
1088A THR* 1.3 74.2 - - - +
1090A LEU* 1.3 59.1 + - - +
1091A ARG 4.1 0.2 - - - -
1136A CYS* 4.5 0.2 - - - -
1202A LEU* 4.1 18.3 - - + +
1206A CYS* 3.7 11.2 - - - -
1211A LEU* 3.6 26.7 - - + -
1212A ARG 2.8 20.5 + - - +
1213A ALA* 3.1 2.9 - - - -
1214A GLY 2.7 32.4 + - - +
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Residues in contact with LEU1090 (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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1021A LEU* 4.4 10.1 - - + -
1022A ALA 2.8 13.8 + - - +
1023A ILE* 3.2 8.6 - - + +
1024A VAL* 2.6 32.2 + - - -
1088A THR* 4.9 0.2 - - + -
1089A PHE* 1.3 81.4 - - - +
1091A ARG* 1.3 58.0 + - - +
1092A ILE 3.8 1.2 + - - -
1136A CYS* 4.0 7.9 - - + -
1140A LEU* 4.4 11.7 - - + -
1214A GLY* 3.7 20.4 - - - +
1245A VAL* 3.6 28.7 - - + +
1248A ALA* 4.4 3.8 - - + -
1249A ALA* 3.7 34.5 - - + +
1252A LEU* 3.8 26.0 - - + -
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Residues in contact with ARG1091 (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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1024A VAL* 3.4 21.1 - - + +
1026A GLY* 3.7 7.5 - - - +
1067A THR* 5.9 1.8 - - + -
1074A THR* 6.3 1.1 - - + -
1089A PHE 4.1 0.2 - - - -
1090A LEU* 1.3 71.5 - - - +
1092A ILE* 1.3 60.7 + - - +
1093A GLY* 3.5 11.7 - - - -
1094A THR 4.6 0.8 + - - -
1196A GLU* 2.9 26.1 + - - +
1198A GLU* 2.8 41.9 + - + +
1199A SER 5.0 0.4 - - - +
1202A LEU* 3.4 27.1 - - + -
1214A GLY 2.8 18.1 + - - +
1215A MET* 3.5 25.4 + - - +
1216A VAL* 2.9 33.9 + - - +
1245A VAL* 4.8 0.6 - - - +
7001A SO4 2.8 39.6 + - - -
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Residues in contact with ILE1092 (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 ILE* 3.8 15.7 - - + -
1024A VAL 4.0 1.4 + - - -
1025A PRO* 3.4 15.7 - - + +
1030A ARG* 2.9 26.7 + - - +
1034A ILE* 3.7 26.9 - - + -
1090A LEU 3.8 1.0 + - - -
1091A ARG* 1.3 78.0 + - - +
1093A GLY* 1.3 66.6 + - - +
1216A VAL* 3.2 6.1 - - + -
1238A GLU* 4.9 2.5 - - + +
1241A ALA* 3.7 31.6 - - + +
1242A VAL* 3.8 24.9 - - + +
1245A VAL* 3.9 19.5 - - + -
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Residues in contact with GLY1093 (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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1030A ARG* 3.4 10.3 - - - -
1091A ARG* 3.5 21.7 - - - +
1092A ILE* 1.3 81.2 - - - +
1094A THR* 1.3 59.3 + - - +
1216A VAL 2.9 9.8 + - - -
1217A ALA* 2.8 7.9 - - - -
1218A GLY 2.8 28.9 + - - -
1241A ALA* 4.8 0.3 - - - +
7001A SO4 3.6 0.4 - - - -
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Residues in contact with THR1094 (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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1030A ARG* 3.5 22.4 - - - +
1091A ARG* 4.6 0.2 + - - -
1092A ILE* 6.2 0.2 - - + -
1093A GLY* 1.3 76.8 - - - +
1095A THR* 1.3 65.5 + - - +
1196A GLU* 4.3 9.0 - - - +
1217A ALA* 4.3 0.5 - - - +
1218A GLY* 3.4 6.7 - - - +
1220A ILE* 3.8 37.3 - - + +
1233A THR* 5.8 0.4 - - + -
1234A MET* 6.1 0.9 - - - -
1238A GLU* 5.0 17.9 - - + +
7001A SO4 2.8 27.3 + - - -
8001A URA 3.7 12.6 + - - -
4048F ARG* 4.8 2.0 + - - +
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Residues in contact with THR1095 (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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1094A THR* 1.3 76.3 - - - +
1096A GLY* 1.3 63.8 + - - +
1108A LEU* 4.3 3.8 - - + -
1194A ASN* 3.0 32.2 + - + +
1195A TYR 2.5 25.0 + - - -
1196A GLU* 4.3 2.5 - - - -
1217A ALA* 3.6 24.7 - - + -
1218A GLY 3.1 17.0 + - - +
1219A VAL* 3.6 14.1 - - + +
1220A ILE* 3.0 28.8 + - - +
1221A VAL 3.7 0.7 + - - -
8001A URA 3.5 11.6 - - - -
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Residues in contact with GLY1096 (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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1095A THR* 1.3 77.6 + - - +
1097A ALA* 1.3 68.0 + - - -
1098A ILE* 3.7 5.9 + - - +
1194A ASN* 3.5 0.3 - - - -
1195A TYR* 3.0 30.1 + - - +
1221A VAL* 3.4 14.4 - - - -
1223A ARG* 4.8 3.6 - - - -
8001A URA 3.4 22.7 - - - -
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Residues in contact with ALA1097 (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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1095A THR* 3.9 2.6 + - - -
1096A GLY* 1.3 73.5 - - - +
1098A ILE* 1.3 62.0 + - - +
1099A GLN 3.7 0.2 - - - -
1102A ILE* 3.9 21.1 - - + -
1193A MET 3.5 10.5 - - - +
1194A ASN* 4.0 3.1 - - - -
1219A VAL* 3.5 28.6 - - + +
1221A VAL 2.8 8.3 + - - +
1222A ASN* 3.4 18.0 - - - +
1223A ARG* 3.0 25.6 + - - +
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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