Contacts of the helix formed by residues 1072 - 1082 (chain A) in PDB entry 5YS0
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 PRO1072 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1070A PRO 4.6 0.9 - - - +
1071A VAL* 1.3 100.3 - - + +
1073A LEU* 1.3 67.2 + - - +
1074A GLY* 3.4 3.1 - - - +
1075A THR* 2.8 35.9 + - + +
1076A VAL* 3.0 7.4 + - - +
1176A ASN* 3.2 40.8 - - + +
1178A THR* 3.2 0.9 + - - -
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Residues in contact with LEU1073 (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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1072A PRO* 1.3 72.7 - - - +
1074A GLY* 1.3 65.3 + - - +
1075A THR 3.0 1.0 + - - -
1076A VAL* 3.1 3.2 + - + +
1077A PHE* 2.9 23.0 + - - +
1140A ASP 5.1 1.1 - - - +
1141A LEU 5.4 2.2 - - - +
1142A ASN* 3.5 27.4 - - - +
1143A SER 3.6 20.4 - - - +
1144A PHE* 3.9 9.9 - - - +
1145A PHE* 3.8 15.4 - - + -
1170A TYR* 3.7 27.8 - - + -
1171A SER 3.8 4.0 - - - +
1172A TRP* 3.9 13.9 - - + +
1176A ASN* 4.5 3.8 + - - +
1177A THR 4.3 2.4 + - - -
1178A THR* 3.0 36.0 + - + +
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Residues in contact with GLY1074 (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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1072A PRO* 3.4 2.6 - - - +
1073A LEU* 1.3 79.1 - - - +
1075A THR* 1.3 59.4 + - - +
1077A PHE* 3.7 9.8 - - - +
1078A SER* 3.1 24.1 + - - -
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Residues in contact with THR1075 (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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1071A VAL* 3.3 25.8 - - + +
1072A PRO* 2.8 34.3 + - + -
1074A GLY* 1.3 76.8 - - - +
1076A VAL* 1.3 55.2 + - - +
1077A PHE 3.1 1.1 - - - -
1078A SER* 3.0 6.7 + - - -
1079A LEU* 2.6 45.8 + - - +
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Residues in contact with VAL1076 (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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1069A ILE* 3.6 33.9 - - + -
1071A VAL* 4.1 12.1 - - + +
1072A PRO 3.0 10.5 + - - +
1073A LEU 3.6 7.0 - - - +
1075A THR* 1.3 80.0 + - - +
1077A PHE* 1.3 65.7 + - - +
1079A LEU* 3.8 8.0 - - + +
1080A LEU* 3.1 34.8 + - + +
1145A PHE* 4.7 2.7 - - + -
1170A TYR* 3.8 36.6 - - + -
1178A THR* 4.3 8.7 - - + +
1217A LEU* 4.6 10.3 - - + -
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Residues in contact with PHE1077 (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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1073A LEU 2.9 11.8 + - - +
1074A GLY* 3.7 13.7 - - - +
1076A VAL* 1.3 77.0 - - - +
1078A SER* 1.3 63.2 + - - +
1081A TYR* 2.8 51.3 + + + +
1082A GLY* 3.2 6.0 + - - -
1136A ILE* 3.8 36.6 - - + -
1139A MET* 4.7 14.8 - - + -
1145A PHE* 3.5 46.2 - + + -
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Residues in contact with SER1078 (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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1074A GLY 3.1 11.3 + - - -
1075A THR* 3.0 11.2 + - - -
1077A PHE* 1.3 83.9 - - - +
1079A LEU* 1.3 60.5 + - - +
1082A GLY* 2.7 35.5 + - - +
1084A ASP* 4.7 5.2 - - - +
1087A TYR* 5.1 1.6 - - - -
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Residues in contact with LEU1079 (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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1071A VAL* 5.3 10.5 - - + -
1075A THR* 2.6 35.0 + - - +
1076A VAL* 3.2 9.8 + - + +
1078A SER* 1.3 75.5 - - - +
1080A LEU* 1.3 62.1 + - - +
1084A ASP 5.0 1.7 - - - +
1087A TYR* 3.2 66.1 - - + +
1088A ILE* 4.1 3.8 + - - +
1217A LEU* 4.5 22.4 - - + +
1220A ILE* 4.7 21.1 - - + -
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Residues in contact with LEU1080 (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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1076A VAL* 3.1 17.0 + - + +
1079A LEU* 1.3 80.5 - - - +
1081A TYR* 1.3 80.8 + - + +
1082A GLY 3.8 0.7 - - - -
1087A TYR* 6.1 0.2 - - + -
1088A ILE* 3.6 27.9 - - + +
1091A ILE* 4.7 9.2 - - + -
1111A ARG* 3.1 19.2 + - - -
1170A TYR* 3.4 32.5 - - + +
1213A LEU* 4.1 26.2 - - + -
1217A LEU* 3.5 43.3 - - + -
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Residues in contact with TYR1081 (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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1077A PHE* 2.8 35.3 + + + +
1080A LEU* 1.3 109.4 - - + +
1082A GLY* 1.3 69.0 + - - +
1083A ASP* 4.8 1.9 - - - +
1088A ILE* 5.5 2.9 - - + -
1106A PHE* 3.4 47.8 - + + -
1111A ARG* 3.8 4.9 - - - +
1134A GLU* 3.6 21.0 + - - -
1136A ILE* 4.8 0.4 - - + -
1145A PHE* 3.7 26.0 - + - -
1147A VAL* 3.4 31.1 - - + +
1168A PHE* 4.0 9.9 - - - +
1170A TYR* 2.8 31.6 + + - -
1213A LEU* 6.1 0.2 - - - +
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Residues in contact with GLY1082 (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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1077A PHE* 3.2 6.3 + - - -
1078A SER* 2.7 35.8 + - - -
1080A LEU 3.8 0.6 - - - -
1081A TYR* 1.3 85.1 - - - +
1083A ASP* 1.3 60.4 + - - -
1084A ASP 3.0 18.6 + - - +
1085A THR* 4.1 9.2 + - - +
1105A LYS* 5.4 1.0 - - - -
1106A PHE* 5.5 0.2 - - - -
1111A ARG* 4.6 3.1 + - - -
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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