Contacts of the strand formed by residues 1062 - 1069 (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 GLY1062 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024A TYR* 5.3 0.9 - - - -
1041A MSE 3.7 1.9 - - - +
1042A TRP* 3.4 11.7 - - - -
1043A LYS 3.2 18.0 + - - -
1060A TYR 4.3 1.2 - - - +
1061A SER* 1.3 77.2 - - - +
1063A VAL* 1.3 66.7 + - - -
1064A SER* 3.4 4.0 + - - -
1097A HIS* 3.7 11.2 - - - -
1098A ASP* 4.4 3.6 - - - -
1101A ASN* 4.0 1.3 - - - -
1102A ILE 3.2 24.7 + - - -
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Residues in contact with VAL1063 (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* 3.8 25.4 - - + -
1041A MSE 3.6 4.7 - - - +
1042A TRP* 3.7 34.5 - - + +
1062A GLY* 1.3 72.0 - - - -
1064A SER* 1.3 60.3 + - - +
1065A LEU* 6.0 0.2 - - - -
1096A TRP* 3.5 28.4 - - + -
1097A HIS* 3.3 4.3 + - - -
1098A ASP* 3.1 30.0 + - + +
1102A ILE 4.4 0.6 + - - +
1125A VAL* 4.5 3.4 - - + -
1127A VAL* 4.1 26.2 - - + -
1134A MSE 5.6 0.7 - - - -
1135A ALA* 4.6 10.5 - - + -
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Residues in contact with SER1064 (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 TYR* 5.4 2.3 + - - -
1039A VAL 3.4 2.1 - - - +
1040A VAL* 3.2 7.8 - - - +
1041A MSE 2.7 44.2 + - - +
1060A TYR 5.3 0.5 + - - -
1062A GLY 3.4 2.3 + - - -
1063A VAL* 1.3 74.3 - - - +
1065A LEU* 1.3 58.5 + - - +
1066A LYS* 3.7 33.1 + - - -
1085A THR* 4.0 5.0 + - - +
1094A THR* 4.8 0.4 - - - +
1096A TRP 3.6 4.5 - - - -
1097A HIS* 2.5 30.1 + - - +
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Residues in contact with LEU1065 (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* 4.2 23.8 - - + -
1038A TYR* 4.6 0.9 - - + -
1039A VAL 3.6 6.1 - - - +
1040A VAL* 4.2 5.2 - - + -
1063A VAL 4.3 0.6 - - - -
1064A SER* 1.3 73.7 - - - +
1066A LYS* 1.3 84.9 + - - +
1094A THR* 3.6 0.5 - - - +
1095A LEU* 2.8 37.6 + - + -
1096A TRP* 2.7 34.1 + - + +
1123A ILE* 3.7 24.9 - - + -
1125A VAL* 4.1 19.3 - - + -
1137A SER* 5.1 0.7 - - - -
1140A ILE* 4.1 28.7 - - + -
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Residues in contact with LYS1066 (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 TYR* 4.3 5.9 + - - -
1038A TYR* 3.2 6.9 - - - +
1039A VAL* 2.7 50.7 + - + +
1041A MSE 3.2 24.7 - - + -
1064A SER* 3.7 25.4 + - - -
1065A LEU* 1.3 85.5 - - - +
1067A VAL* 1.3 60.1 + - - +
1068A VAL 4.1 0.2 - - - -
1082A LEU* 3.0 27.3 + - + +
1084A HIS 3.6 17.5 + - - -
1085A THR* 4.5 3.0 + - - +
1092A VAL* 3.8 19.7 - - + -
1093A ARG 3.5 6.5 - - - +
1094A THR* 3.2 26.7 - - + +
1095A LEU* 4.3 2.0 - - - +
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Residues in contact with VAL1067 (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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1037A PHE 3.7 2.5 - - - +
1038A TYR* 3.7 27.8 - - + -
1066A LYS* 1.3 73.8 - - - +
1068A VAL* 1.3 66.4 + - - +
1069A ASN* 3.6 2.4 + - + +
1092A VAL* 4.6 1.1 - - - -
1093A ARG* 2.8 72.0 + - + +
1095A LEU* 3.9 13.0 - - + -
1142A ASP* 4.3 0.7 - - - +
1144A THR* 3.9 13.7 - - + +
1145A TYR* 3.6 26.2 - - + -
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Residues in contact with VAL1068 (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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1034A SER 4.1 0.2 - - - +
1035A SER* 3.3 27.6 - - - +
1037A PHE* 2.8 54.4 + - + +
1039A VAL* 4.5 5.4 - - + -
1067A VAL* 1.3 71.0 - - - +
1069A ASN* 1.3 54.8 + - - +
1070A SER 4.1 1.8 - - - +
1078A LEU* 3.7 21.5 - - + -
1082A LEU* 3.7 20.0 - - + -
1091A GLN 3.7 3.6 - - - -
1092A VAL* 3.9 10.3 - - + -
1145A TYR* 2.6 33.3 + - - -
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Residues in contact with ASN1069 (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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1035A SER 3.4 4.8 - - - +
1036A ARG* 5.0 4.9 + - - +
1067A VAL* 3.6 4.4 + - + +
1068A VAL* 1.3 73.7 - - - +
1070A SER* 1.3 62.6 + - - +
1071A THR* 3.8 1.4 + - - +
1090A GLY* 3.5 13.7 - - - +
1091A GLN 2.8 15.6 + - - +
1093A ARG* 5.2 10.1 - - - +
1144A THR* 4.8 7.6 - - + +
1145A TYR* 3.5 11.1 + - + +
1C NAG 1.4 65.4 + - - +
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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