Contacts of the strand formed by residues 1048 - 1055 (chain N) in PDB entry 3O3U
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 ARG1048 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1042N PRO* 5.3 2.7 - - - +
1047N GLN* 1.3 69.9 - - - +
1049N LEU* 1.3 60.7 + - - +
1100N GLN 4.0 0.2 - - - +
1101N ALA* 3.6 1.4 - - - +
1102N MET* 2.9 65.2 + - + +
1103N ASN 6.1 0.2 - - - -
6581N SO4 5.5 1.0 + - - -
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Residues in contact with LEU1049 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038N CYS* 4.1 11.4 - - - -
1041N ALA* 4.0 12.1 - - + -
1047N GLN* 3.6 29.7 + - + +
1048N ARG* 1.3 76.4 - - - +
1050N GLU* 1.3 65.8 + - - +
1051N TRP* 3.7 28.5 - - + +
1078N VAL* 4.4 12.3 - - + -
1082N GLY* 3.8 29.2 - - - +
1099N CYS* 4.3 0.9 - - - -
1100N GLN 3.1 11.9 - - - +
1101N ALA* 4.3 3.6 - - + -
1102N MET* 6.0 0.2 - - - -
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Residues in contact with GLU1050 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049N LEU* 1.3 77.9 - - - +
1051N TRP* 1.3 66.7 + - - +
1052N LYS* 4.7 11.2 + - + +
1063N VAL* 3.6 39.0 - - + +
1064N LEU 5.3 1.8 - - - +
1098N ARG 3.7 0.9 - - - +
1099N CYS* 3.3 5.2 - - - -
1100N GLN* 3.0 45.9 + - + +
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Residues in contact with TRP1051 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036N LEU* 3.4 38.6 - - + -
1037N LYS 3.7 11.4 - - - -
1038N CYS* 3.7 11.2 - - + -
1049N LEU* 3.7 14.0 - - + +
1050N GLU* 1.3 74.4 - - - +
1052N LYS* 1.3 63.6 + - - +
1063N VAL* 3.6 5.7 - - - +
1064N LEU* 2.9 49.5 + - + -
1078N VAL* 3.6 23.6 - - + -
1082N GLY 2.8 19.8 + - - -
1083N SER 4.1 0.4 - - - -
1084N LEU* 3.6 33.3 - - + +
1097N PHE* 4.4 3.6 - - + -
1098N ARG 3.3 32.5 - - - -
1099N CYS* 3.5 25.7 - - + -
1113N TYR* 4.0 13.0 - + - -
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Residues in contact with LYS1052 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050N GLU* 4.7 14.7 + - + +
1051N TRP* 1.3 78.9 - - - +
1053N LEU* 1.3 66.3 + - - +
1061N TRP* 3.8 27.4 - - + -
1062N LYS 3.1 14.6 - - - +
1063N VAL* 4.1 15.5 - - + -
1064N LEU* 5.9 0.2 - - - -
1084N LEU* 6.5 0.2 - - - -
1097N PHE* 3.6 1.4 - - - +
1098N ARG* 2.8 69.8 + - + +
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Residues in contact with LEU1053 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052N LYS* 1.3 78.9 - - - +
1054N ASN* 1.3 62.6 + - - +
1055N THR* 4.0 11.2 - - + +
1058N THR* 4.0 5.7 + - + -
1060N ALA 3.6 0.9 - - - +
1061N TRP* 3.5 5.8 - - - -
1062N LYS* 2.9 65.5 + - + +
1064N LEU* 4.0 20.4 - - + -
1072N TRP* 3.9 25.1 - - + -
1076N ALA* 5.1 4.9 - - + -
1084N LEU* 5.8 0.4 - - + -
1086N LEU* 6.2 0.2 - - + -
1093N ASP* 5.9 2.0 - - - +
1096N ILE 3.2 12.8 - - - +
1097N PHE* 3.5 37.2 - - + -
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Residues in contact with ASN1054 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1053N LEU* 1.3 77.3 - - - +
1055N THR* 1.3 63.5 + - - +
1058N THR* 3.5 4.5 + - - -
1059N GLU 4.4 3.8 - - - +
1060N ALA* 3.4 28.9 - - - +
1061N TRP* 3.4 43.2 - - + +
1095N GLY* 3.3 4.0 - - - -
1096N ILE* 2.9 35.1 + - + +
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Residues in contact with THR1055 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1053N LEU* 4.0 13.1 - - + +
1054N ASN* 1.3 84.9 - - - +
1056N GLY* 1.3 61.1 + - - +
1057N ARG* 3.1 22.1 + - - +
1058N THR* 3.0 34.7 + - - +
1092N GLN 3.4 10.4 + - - -
1093N ASP* 3.4 20.4 + - - +
1094N GLU 3.4 11.7 - - - +
1095N GLY* 4.1 1.6 - - - -
1097N PHE* 3.7 24.5 - - + -
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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