Contacts of the strand formed by residues 1016 - 1023 (chain A) in PDB entry 1FO4
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 GLN1016 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1013A PHE 2.7 24.1 + - - +
1014A LEU 2.8 11.1 + - - +
1015A ASN* 1.3 74.8 - - - +
1017A ALA* 1.3 63.3 + - - +
1073A ASN* 4.5 8.5 - - - +
1074A SER* 5.8 0.3 - - - -
1075A SER* 3.9 17.9 + - - +
1085A ILE* 3.7 9.6 - - - +
1086A TYR* 4.7 2.1 + - - -
1132A PHE* 3.4 30.9 - - + -
1133A TYR 3.2 7.9 - - - +
1121B TYR* 3.3 52.8 + - - -
1124B ARG* 3.6 18.3 - - + +
1125B VAL 4.7 2.8 + - - +
1126B SER* 5.5 0.2 - - - -
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Residues in contact with ALA1017 (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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1016A GLN* 1.3 77.5 - - - +
1018A GLY* 1.3 59.3 + - - +
1074A SER* 6.5 0.7 - - - +
1085A ILE* 3.5 33.2 - - + +
1086A TYR* 3.4 31.2 - - + -
1089A ALA* 3.5 2.6 - - - +
1132A PHE* 3.2 12.4 - - - -
1133A TYR 3.0 32.6 + - - +
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Residues in contact with GLY1018 (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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1017A ALA* 1.3 75.6 - - - +
1019A ALA* 1.3 62.0 + - - +
1033A HIS* 3.6 1.0 - - - -
1034A GLY 3.3 22.0 + - - -
1071A VAL* 3.8 19.3 - - - +
1086A TYR* 3.8 8.9 - - - -
1089A ALA* 3.9 2.0 - - - -
1131A GLY 3.2 8.1 - - - -
1132A PHE* 4.0 9.5 - - - -
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Residues in contact with ALA1019 (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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1018A GLY* 1.3 74.2 - - - +
1020A LEU* 1.3 63.0 - - - +
1021A ILE* 5.2 1.3 - - + -
1032A SER 3.2 11.7 - - - +
1033A HIS* 4.3 1.8 - - + -
1071A VAL* 4.0 5.3 - - - +
1089A ALA* 3.8 31.0 - - + +
1090A VAL* 3.9 18.4 - - + +
1093A ALA* 4.9 3.1 - - + -
1130A THR* 3.1 9.7 - - - +
1131A GLY* 2.8 28.0 + - - +
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Residues in contact with LEU1020 (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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1019A ALA* 1.3 74.5 - - - +
1021A ILE* 1.3 63.3 + - - +
1022A HIS* 3.7 34.3 - - + +
1030A LEU 3.9 1.2 - - - +
1031A VAL* 3.7 0.7 - - - -
1032A SER* 2.7 42.2 + - - +
1070A THR* 3.7 34.5 - - + +
1071A VAL* 4.3 2.7 - - + -
1128A SER* 4.1 5.4 - - - +
1129A THR 3.5 18.8 - - - +
1130A THR* 4.0 17.5 - - + -
1020B LEU* 3.7 28.5 - - + -
1069B ASN 4.1 6.7 - - - +
1130B THR* 4.5 1.1 - - + -
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Residues in contact with ILE1021 (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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1019A ALA* 5.2 0.9 - - + -
1020A LEU* 1.3 81.9 - - - +
1022A HIS* 1.3 69.8 + - - +
1023A VAL* 4.7 5.8 - - + -
1029A VAL* 3.3 29.6 - - + -
1030A LEU 3.5 4.7 - - - +
1031A VAL* 3.8 23.8 - - + -
1054A LEU* 5.8 2.0 - - + -
1090A VAL* 3.8 19.1 - - + +
1093A ALA* 3.5 28.5 - - + -
1094A CYS* 3.8 19.3 - - - +
1097A ILE* 4.5 11.6 - - + +
1127A LEU 3.8 1.2 - - - +
1128A SER* 3.4 4.3 - - - -
1129A THR* 3.0 34.2 + - - +
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Residues in contact with HIS1022 (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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1020A LEU* 3.7 24.1 - - + +
1021A ILE* 1.3 74.9 + - - +
1023A VAL* 1.3 63.0 + - - +
1024A TYR* 3.7 27.1 + - + -
1028A SER 4.2 0.2 - - - +
1029A VAL* 3.3 6.6 - - - +
1030A LEU* 3.0 42.0 + - + +
1127A LEU 3.5 4.5 - - - -
1128A SER* 2.8 29.1 + - - -
1068B THR 4.1 2.0 - - - -
1069B ASN* 2.8 33.7 + - - -
1070B THR 3.4 18.1 - - - -
1072B PRO* 3.5 25.4 - - + +
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Residues in contact with VAL1023 (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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1021A ILE* 4.7 1.8 - - + -
1022A HIS* 1.3 78.4 - - - +
1024A TYR* 1.3 74.0 + - - +
1027A GLY 4.0 5.4 - - - +
1028A SER 3.6 8.7 - - - +
1029A VAL* 4.0 16.8 - - + -
1054A LEU* 5.7 1.1 - - + -
1097A ILE* 4.2 29.4 - - + -
1113A TRP* 4.0 11.7 - - + -
1117A VAL* 3.7 28.3 - - + -
1127A LEU* 3.1 27.7 + - + +
1073B ASN* 3.1 21.4 + - - -
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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