Contacts of the strand formed by residues 1042 - 1048 (chain A) in PDB entry 5DGY
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 VAL1042 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1027A LEU* 3.6 25.4 - - + -
1032A TYR* 3.6 15.9 - - + +
1041A PRO* 1.3 71.6 - - - +
1043A ASP* 1.3 63.4 + - - +
1062A LEU* 4.2 7.9 - - + -
1119A PHE* 4.1 12.7 - - + +
1120A LEU* 3.5 10.6 - - - +
1121A LEU* 2.8 44.0 + - + +
1123A PHE* 3.4 30.3 - - + -
1150A VAL* 4.2 11.2 - - + -
1175A ILE* 3.6 16.6 - - + -
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Residues in contact with ASP1043 (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 LEU* 3.4 15.2 - - - +
1028A GLY* 3.8 3.6 + - - -
1029A LYS* 5.1 4.1 - - - +
1032A TYR* 3.3 22.4 + - - -
1041A PRO* 3.9 4.9 - - + +
1042A VAL* 1.3 78.0 - - - +
1044A GLY* 1.3 58.5 + - - +
1102A THR* 4.3 18.7 + - + +
1104A LEU* 3.3 34.5 - - + +
1105A GLN* 4.8 2.9 - - - +
1119A PHE 3.8 5.4 - - - +
1120A LEU* 4.3 13.0 - - + -
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Residues in contact with GLY1044 (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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1026A TYR 3.4 13.0 - - - -
1027A LEU* 4.6 0.2 - - - -
1043A ASP* 1.3 76.9 - - - +
1045A VAL* 1.3 68.7 + - - +
1104A LEU* 4.6 7.4 - - - -
1105A GLN* 3.6 8.5 + - - +
1108A LEU* 4.8 3.6 - - - -
1118A PRO* 3.5 0.9 - - - +
1119A PHE* 2.9 41.7 + - - +
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Residues in contact with VAL1045 (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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1026A TYR* 2.8 48.9 + - + +
1044A GLY* 1.3 79.9 - - - +
1046A VAL* 1.3 67.6 + - - +
1105A GLN* 4.4 13.2 - - + +
1108A LEU* 3.9 25.6 - - + -
1109A LEU* 5.0 2.7 - - + -
1112A LEU* 3.9 11.0 - - + -
1116A THR* 3.5 29.4 - - + -
1117A TYR 3.4 7.0 - - - +
1118A PRO* 3.8 17.7 - - + -
1119A PHE* 3.5 3.2 - - - -
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Residues in contact with VAL1046 (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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1023A VAL* 4.8 7.4 - - + -
1024A THR 3.5 4.3 - - - +
1025A ILE* 3.7 26.9 - - + +
1045A VAL* 1.3 80.4 - - - +
1047A LEU* 1.3 64.5 + - - +
1048A VAL* 3.8 8.8 - - + +
1058A VAL* 5.3 3.6 - - + -
1060A VAL* 4.8 2.2 - - + -
1091A VAL* 3.5 33.7 - - + -
1115A ASN 3.7 2.1 - - - +
1116A THR* 3.7 3.3 - - - -
1117A TYR 2.9 33.6 + - - +
1119A PHE* 4.0 10.8 - - + -
1152A ALA* 4.1 18.2 - - + -
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Residues in contact with LEU1047 (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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1022A SER 3.7 1.3 - - - +
1023A VAL* 3.5 5.5 - - - +
1024A THR* 2.9 41.7 + - + +
1026A TYR* 3.8 34.7 - - + +
1046A VAL* 1.3 72.8 - - - +
1048A VAL* 1.3 65.5 + - - +
1112A LEU* 4.8 7.9 - - + -
1113A GLY* 5.1 8.7 - - - +
1115A ASN* 3.6 26.9 - - + +
1116A THR* 3.6 18.8 - - - +
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Residues in contact with VAL1048 (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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1022A SER 3.8 5.2 - - - +
1023A VAL* 5.0 4.3 - - + -
1046A VAL* 3.8 15.7 - - + +
1047A LEU* 1.3 85.5 - - - +
1049A ASP* 1.3 66.0 + - - +
1050A PRO* 3.5 1.9 - - - +
1053A VAL* 3.5 37.5 - - + -
1058A VAL* 4.3 22.7 - - + -
1092A TYR* 4.3 11.7 - - + -
1115A ASN* 3.1 33.6 + - + +
1117A TYR* 4.0 22.0 - - + -
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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