Contacts of the strand formed by residues 1110 - 1116 (chain A) in PDB entry 1YO8
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 TYR1110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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697A LEU* 3.5 4.0 - - - -
1013A THR* 3.2 10.6 - - - +
1014A PHE* 2.8 47.9 + + + +
1042A TRP* 3.5 37.2 - + + -
1103A GLY 4.2 0.3 + - - -
1104A TRP* 3.6 15.6 - - + -
1105A LYS* 3.0 42.9 + - - +
1108A THR* 3.3 33.2 - - + -
1109A ALA* 1.3 72.6 - - - +
1111A ARG* 1.3 59.4 + - - +
1127A VAL* 4.1 5.2 - - + -
1128A HIS 3.1 18.2 - - - +
1129A GLU* 3.6 23.1 - - + -
1134A MSE 3.0 27.4 - - + +
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Residues in contact with ARG1111 (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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682A THR* 3.5 38.7 + - + +
697A LEU* 3.6 10.4 + - + +
1011A SER* 3.4 28.2 + - - -
1012A GLY 3.4 11.3 - - - +
1013A THR* 3.0 32.5 + - - +
1110A TYR* 1.3 73.7 - - - +
1112A TRP* 1.3 67.2 + - - +
1113A HIS* 6.0 0.9 - - + -
1126A LEU 3.8 0.3 - - - +
1127A VAL* 3.3 4.6 - - - -
1128A HIS* 2.6 41.1 + - + +
1163A SER 3.5 1.6 + - - -
1164A ASP* 2.9 41.2 + - - +
1166A LYS* 3.3 20.6 - - - +
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Residues in contact with TRP1112 (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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1010A PHE* 3.5 25.1 + + - -
1011A SER* 3.0 32.4 - - - +
1012A GLY* 3.0 51.6 + - - +
1013A THR 4.0 4.9 - - - -
1014A PHE* 3.9 31.2 - + + -
1026A GLY* 5.3 0.9 - - - -
1027A PHE* 3.1 52.2 - + + -
1110A TYR 4.3 0.2 - - - -
1111A ARG* 1.3 77.6 - - - +
1113A HIS* 1.3 61.5 + - - +
1114A LEU 4.1 0.2 - - - -
1125A VAL* 5.3 1.1 - - + -
1126A LEU 3.1 7.9 - - - +
1127A VAL* 4.1 14.1 - - + +
1128A HIS* 6.0 0.2 - - - -
1152A LEU* 3.7 26.0 - - + -
1162A PHE* 3.8 16.4 - + + -
1165A LEU* 3.8 14.1 - - + -
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Residues in contact with HIS1113 (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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1009A ASP* 3.9 30.0 + - + +
1010A PHE 3.6 5.4 - - - -
1011A SER* 3.6 24.5 - - - -
1111A ARG* 6.0 0.9 - - + -
1112A TRP* 1.3 75.5 - - - +
1114A LEU* 1.3 59.7 + - - +
1115A THR* 3.6 23.4 + - - -
1124A ARG 3.3 4.7 - - - +
1125A VAL* 3.5 3.1 - - - -
1126A LEU* 2.6 59.5 + - + +
1128A HIS* 5.8 3.8 - - + -
1170A ARG* 5.9 0.8 + - - -
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Residues in contact with LEU1114 (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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1008A VAL* 4.3 7.4 - - + -
1009A ASP* 3.1 8.7 - - - +
1010A PHE* 2.6 54.9 + - + +
1027A PHE* 4.0 19.3 - - + -
1029A PHE* 3.4 65.3 - - + -
1112A TRP* 4.1 1.6 - - - -
1113A HIS* 1.3 74.9 - - - +
1115A THR* 1.3 75.2 + - - +
1116A HIS* 4.0 9.4 - - + -
1123A ILE* 4.0 9.2 - - + -
1124A ARG 3.4 4.0 - - - +
1125A VAL* 4.4 8.1 - - + +
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Residues in contact with THR1115 (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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1009A ASP* 3.5 4.2 + - - +
1113A HIS* 3.6 20.4 + - - -
1114A LEU* 1.3 77.2 - - - +
1116A HIS* 1.3 58.9 + - - +
1117A ARG* 3.5 33.4 - - + +
1122A TYR* 3.7 22.0 - - + -
1123A ILE* 3.3 5.4 - - - -
1124A ARG* 2.8 51.7 + - - +
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Residues in contact with HIS1116 (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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1006A GLY 4.4 2.0 + - - -
1007A SER* 3.4 2.6 - - - -
1008A VAL* 2.8 57.6 + - + +
1029A PHE* 3.4 33.4 - + + -
1030A GLY* 5.0 3.4 + - - -
1038A TYR* 4.2 11.0 + + - -
1114A LEU* 4.0 5.1 - - + -
1115A THR* 1.3 74.4 - - - +
1117A ARG* 1.3 76.6 + - - +
1118A PRO* 3.5 34.2 - - + +
1121A GLY 5.1 0.7 - - - -
1122A TYR 3.4 9.9 - - - -
1123A ILE* 3.7 16.2 - - + +
1142A ASP 4.9 3.4 + - - -
1145A TYR 4.0 13.7 + - - -
1147A GLY* 4.4 9.8 - - - -
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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