Contacts of the helix formed by residues 1088 - 1101 (chain D) in PDB entry 1ZYR
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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706D PRO* 6.4 2.2 - - + -
1084D THR* 2.8 22.6 + - - -
1085D ALA* 4.3 6.9 - - - -
1086D LEU 2.9 0.6 - - - -
1087D ARG* 1.3 75.3 - - - +
1089D ALA* 1.3 69.6 + - - +
1091D SER* 3.4 2.9 - - - -
1092D GLY* 3.2 14.2 + - - -
1234D THR* 3.4 26.7 + - + +
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Residues in contact with ALA1089 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085D ALA 4.0 11.1 + - - +
1086D LEU* 2.8 11.1 + - - +
1088D THR* 1.3 75.1 - - - +
1090D ASP* 1.3 64.2 + - - +
1091D SER 3.0 1.1 - - - -
1092D GLY* 2.7 26.2 + - - -
1093D TYR* 2.9 17.7 + - + -
1525D STD 4.7 11.2 - - + -
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Residues in contact with ASP1090 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086D LEU* 3.0 43.2 + - - +
1087D ARG* 4.8 0.6 - - - -
1089D ALA* 1.3 78.5 - - - +
1091D SER* 1.3 66.7 + - - +
1093D TYR* 3.2 19.7 - - + +
1094D LEU* 2.9 21.8 + - - +
1256D LEU* 4.3 14.8 - - + +
1260D ILE* 4.9 7.4 - - + +
1525D STD 3.3 35.8 + - - +
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Residues in contact with SER1091 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087D ARG 2.8 25.4 + - - -
1088D THR* 3.4 7.6 - - - -
1089D ALA 2.9 0.6 + - - -
1090D ASP* 1.3 80.9 - - - +
1092D GLY* 1.3 70.5 + - - +
1094D LEU* 2.9 7.1 + - - +
1095D THR* 2.9 18.6 + - - -
1230D GLY 3.6 20.1 + - - -
1233D GLY* 4.1 2.5 - - - -
1234D THR* 3.8 21.4 + - - -
1256D LEU* 3.8 13.4 - - - +
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Residues in contact with GLY1092 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035C MET* 6.0 6.5 - - - -
1038C TRP* 5.4 1.1 - - - -
1088D THR 3.2 6.1 + - - -
1089D ALA 2.7 11.9 + - - -
1091D SER* 1.3 74.6 + - - +
1093D TYR* 1.3 56.9 + - - +
1095D THR* 2.5 35.9 + - - -
1096D ARG* 3.0 11.8 + - - -
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Residues in contact with TYR1093 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615D ARG* 5.1 14.8 + - - -
1089D ALA* 2.9 16.7 + - + -
1090D ASP* 3.2 30.1 - - - +
1092D GLY* 1.3 71.2 - - - +
1094D LEU* 1.3 59.1 + - - +
1096D ARG* 2.9 34.8 + - - +
1097D LYS* 3.3 27.5 + - + +
1525D STD 5.9 4.3 - - - -
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Residues in contact with LEU1094 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090D ASP 2.9 9.9 + - - +
1091D SER* 3.3 10.1 - - - +
1092D GLY 2.8 2.4 + - - -
1093D TYR* 1.3 72.8 - - - +
1095D THR* 1.3 64.8 + - - +
1096D ARG 2.9 5.9 + - - -
1097D LYS* 3.0 22.0 + - + +
1098D LEU* 2.9 61.0 + - + +
1229D ILE 4.8 7.0 - - - +
1230D GLY* 5.5 0.9 - - - -
1256D LEU* 4.9 6.5 - - + -
1259D VAL* 4.7 5.4 - - + -
1260D ILE* 3.6 33.4 - - + -
1263D PHE* 4.3 25.4 - - + -
1356D TYR* 5.1 1.3 - - - +
1424D VAL* 5.5 0.9 - - + -
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Residues in contact with THR1095 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038C TRP* 4.0 21.1 - - + -
708D LEU 5.8 2.0 - - - +
1091D SER* 2.9 13.9 + - - -
1092D GLY* 2.5 17.4 + - - -
1094D LEU* 1.3 76.1 - - - +
1096D ARG* 1.3 57.2 + - - -
1098D LEU* 3.8 7.8 - - - +
1099D VAL* 2.9 35.6 + - + +
1226D ALA* 4.3 12.1 - - + +
1227D GLN* 4.8 5.2 - - + -
1230D GLY* 3.6 36.4 + - - -
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Residues in contact with ARG1096 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034C GLU* 2.8 39.9 + - - -
1035C MET* 5.3 3.6 - - - +
1038C TRP* 3.6 20.3 - - + -
614D PHE* 6.0 6.4 - - - -
615D ARG* 2.9 41.4 - - - +
1092D GLY 3.0 4.8 + - - -
1093D TYR* 2.9 27.8 + - - +
1095D THR* 1.3 75.8 - - - +
1097D LYS* 1.3 65.6 + - + +
1099D VAL* 3.1 3.6 + - - +
1100D ASP* 2.5 45.4 + - - +
1439D SER 5.6 4.7 - - - -
1463D LYS* 5.9 1.3 - - - +
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Residues in contact with LYS1097 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093D TYR* 3.3 26.6 + - + +
1094D LEU* 3.0 25.0 + - + +
1096D ARG* 1.3 77.5 - - + +
1098D LEU* 1.3 64.5 + - + +
1100D ASP* 3.0 11.3 + - - +
1101D VAL* 3.0 25.2 + - - +
1260D ILE* 4.6 13.3 - - - +
1264D GLU* 3.0 26.9 + - - +
1266D ARG* 5.0 1.0 - - - +
1424D VAL* 3.6 18.6 - - + -
1425D THR* 3.4 25.7 + - - +
1440D PHE* 6.2 0.7 - - - -
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Residues in contact with LEU1098 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094D LEU* 2.9 57.0 + - + +
1095D THR* 3.8 8.3 - - - +
1097D LYS* 1.3 81.3 - - + +
1099D VAL* 1.3 61.0 + - - +
1101D VAL* 3.3 2.9 + - - +
1102D THR* 2.6 32.6 + - - +
1226D ALA* 3.6 33.0 - - + +
1229D ILE* 4.3 20.9 - - + +
1230D GLY* 5.0 0.4 - - - +
1263D PHE* 4.6 13.7 - - + -
1371D VAL* 4.7 15.5 - - + -
1424D VAL* 4.3 12.8 - - + -
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Residues in contact with VAL1099 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038C TRP* 3.7 45.8 - - + +
1041C GLU* 4.6 4.5 - - - +
1095D THR* 2.9 20.0 - - + +
1096D ARG 3.1 5.0 + - - +
1098D LEU* 1.3 75.3 - - - +
1100D ASP* 1.3 58.5 + - - +
1102D THR* 3.6 3.1 - - - -
1103D HIS* 2.9 39.6 + - + +
1223D ILE* 3.9 27.6 - - + +
1226D ALA* 3.8 17.9 - - + -
1227D GLN* 5.4 1.6 - - + +
1463D LYS* 5.2 5.2 - - - +
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Residues in contact with ASP1100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038C TRP* 5.3 0.3 - - - -
1096D ARG* 2.5 41.7 - - - +
1097D LYS* 3.1 12.3 - - - +
1099D VAL* 1.3 75.7 - - - +
1101D VAL* 1.3 58.9 + - - +
1102D THR 3.0 5.1 + - - -
1103D HIS* 3.1 27.3 + - - -
1428D ALA* 4.1 9.6 - - + +
1431D THR* 5.4 3.5 - - - +
1436D SER* 4.6 1.2 + - - -
1439D SER 4.8 4.3 - - - +
1440D PHE* 3.0 42.4 - - + -
1463D LYS* 3.9 22.5 + - - +
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Residues in contact with VAL1101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097D LYS* 3.0 16.2 + - - +
1098D LEU* 4.1 3.4 - - - +
1100D ASP* 1.3 73.6 - - - +
1102D THR* 1.3 61.4 + - - +
1104D GLU* 5.8 2.2 - - - -
1371D VAL* 5.2 3.1 - - + +
1374D GLN* 3.3 36.9 - - + +
1375D MET* 5.1 0.7 - - + +
1377D LYS* 4.3 9.0 + - - +
1424D VAL* 3.1 41.7 - - + +
1425D THR* 5.1 0.4 - - - -
1427D SER* 3.4 26.2 - - - +
1428D ALA* 3.3 18.2 - - + +
1431D THR* 6.0 0.9 - - - -
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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