Contacts of the strand formed by residues 1122 - 1129 (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 TYR1122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1115A THR* 3.7 31.2 - - + -
1116A HIS* 3.4 3.3 - - - -
1117A ARG* 2.8 44.2 + - + -
1120A THR* 3.3 16.4 + - - +
1121A GLY* 1.3 75.7 - - - +
1123A ILE* 1.3 65.9 + - - +
1124A ARG* 3.5 40.7 + - + +
1139A PRO* 3.7 28.1 - - + +
1140A ILE 3.4 6.3 - - - -
1141A TYR* 3.4 30.7 - + + +
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Residues in contact with ILE1123 (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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1029A PHE* 3.8 22.4 - - + -
1038A TYR* 3.8 32.3 - - + -
1065A LEU* 3.7 22.0 - - + -
1095A LEU* 4.6 6.7 - - + -
1114A LEU* 4.0 11.9 - - + -
1115A THR 3.3 3.6 - - - -
1116A HIS* 3.7 14.8 - - + -
1121A GLY 3.8 3.6 - - - +
1122A TYR* 1.3 83.3 - - - +
1124A ARG* 1.3 67.1 + - - +
1125A VAL* 4.2 3.6 - - + -
1138A GLY 3.6 1.2 - - - +
1139A PRO* 3.7 1.4 - - - +
1140A ILE* 2.8 50.1 + - + +
1142A ASP* 4.2 16.2 - - + +
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Residues in contact with ARG1124 (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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1113A HIS 3.3 4.2 - - - +
1114A LEU* 3.4 2.1 - - - +
1115A THR* 2.8 46.6 + - - +
1122A TYR* 3.5 32.5 + - + +
1123A ILE* 1.3 75.8 - - - +
1125A VAL* 1.3 65.0 + - - +
1126A LEU* 3.2 32.3 - - + +
1136A ASP* 2.8 41.4 + - - +
1137A SER* 3.6 3.8 - - - -
1138A GLY* 3.9 17.2 - - - +
1139A PRO* 4.2 3.5 - - - +
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Residues in contact with VAL1125 (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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1027A PHE* 4.7 8.7 - - + -
1040A VAL* 4.0 40.4 - - + -
1063A VAL* 4.5 6.7 - - + -
1065A LEU* 4.1 22.2 - - + -
1096A TRP* 4.8 4.4 - - + -
1112A TRP* 5.3 0.2 - - + -
1113A HIS 3.5 5.2 - - - +
1114A LEU* 4.4 5.2 - - + -
1123A ILE* 4.2 7.0 - - + -
1124A ARG* 1.3 75.9 - - - +
1126A LEU* 1.3 69.0 + - - +
1127A VAL* 4.4 12.1 - - + +
1135A ALA 3.8 1.2 - - - +
1136A ASP* 3.5 4.9 - - - +
1137A SER* 3.0 37.9 + - - +
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Residues in contact with LEU1126 (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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1111A ARG 3.8 0.6 - - - +
1112A TRP* 3.1 4.2 - - - +
1113A HIS* 2.6 62.0 + - + +
1124A ARG* 3.2 47.6 - - + +
1125A VAL* 1.3 74.4 - - - +
1127A VAL* 1.3 63.0 + - - +
1128A HIS* 4.3 23.6 - - + +
1133A VAL* 5.2 8.5 - - + -
1135A ALA 3.4 3.4 - - - +
1136A ASP* 3.3 23.1 - - + +
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Residues in contact with VAL1127 (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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1040A VAL* 5.7 1.3 - - + -
1042A TRP* 3.8 33.0 - - + -
1063A VAL* 4.1 22.0 - - + -
1110A TYR* 4.1 4.3 - - + -
1111A ARG 3.3 7.9 - - - +
1112A TRP* 4.1 14.6 - - + +
1125A VAL* 4.4 12.3 - - + -
1126A LEU* 1.3 80.0 - - - +
1128A HIS* 1.3 73.8 + - - +
1133A VAL* 3.8 3.3 - - - +
1134A MSE 2.9 29.4 + - + -
1135A ALA* 2.9 26.0 + - + +
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Residues in contact with HIS1128 (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* 3.9 30.8 + - + -
1110A TYR* 3.1 14.6 - - - +
1111A ARG* 2.6 40.7 + - + +
1113A HIS* 5.8 4.3 - - + -
1126A LEU* 4.3 21.7 - - + +
1127A VAL* 1.3 78.6 - - - +
1129A GLU* 1.3 58.6 + - - +
1130A GLY 3.9 11.8 + - - +
1131A LYS 3.3 25.0 + - - -
1132A GLN 3.6 3.3 - - - -
1133A VAL* 3.3 33.3 + - + +
1134A MSE 4.2 0.7 - - - -
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Residues in contact with GLU1129 (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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1105A LYS* 2.5 39.3 + - - -
1108A THR* 4.1 8.1 - - + +
1109A ALA 4.1 4.3 - - - +
1110A TYR* 3.6 27.3 - - + -
1128A HIS* 1.3 70.6 - - - +
1130A GLY* 1.3 69.4 + - - +
1131A LYS 3.1 0.3 + - - -
1132A GLN* 2.9 36.4 + - + +
1134A MSE 3.9 21.3 - - + +
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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