Contacts of the strand formed by residues 1108 - 1118 (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 GLU1108 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1100N GLN* 2.8 35.2 + - + +
1101N ALA 3.4 4.0 - - - -
1102N MET* 3.4 24.7 - - + +
1106N GLY 3.5 2.7 + - - +
1107N LYS* 1.3 79.7 - - - +
1109N THR* 1.3 71.6 + - - +
1110N LYS* 3.9 23.4 + - + +
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Residues in contact with THR1109 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1038N CYS* 5.7 0.2 - - - -
1039N LYS* 3.4 44.3 - - + +
1040N GLY* 4.1 10.4 - - - +
1099N CYS 3.8 0.5 - - - +
1100N GLN* 3.5 3.6 - - - +
1101N ALA* 2.9 34.7 + - - +
1103N ASN* 4.8 2.1 + - - -
1107N LYS* 4.3 18.4 + - - +
1108N GLU* 1.3 77.8 + - - +
1110N LYS* 1.3 71.0 + - - +
1111N SER 4.2 0.3 + - - -
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Residues in contact with LYS1110 (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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1039N LYS* 4.0 11.4 + - - -
1099N CYS 3.3 8.3 - - - +
1100N GLN* 4.5 8.5 - - + +
1108N GLU* 3.9 28.4 + - + +
1109N THR* 1.3 81.7 - - - +
1111N SER* 1.3 62.9 + - - +
1112N ASN* 4.4 2.6 + - + -
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Residues in contact with SER1111 (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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1037N LYS 3.8 4.7 - - - -
1038N CYS* 4.0 0.7 - - - -
1039N LYS* 2.9 54.5 + - - +
1098N ARG* 3.2 8.2 - - - +
1099N CYS* 2.9 39.7 + - - +
1109N THR 4.2 0.2 + - - -
1110N LYS* 1.3 73.9 - - - +
1112N ASN* 1.3 61.6 + - - +
1113N TYR* 3.7 20.2 - - - -
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Residues in contact with ASN1112 (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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371N ALA* 3.9 16.9 + - + +
372N SER 2.9 28.4 + - - +
1023N ALA* 3.4 13.7 - - - +
1024N GLN* 2.8 26.7 + - - +
1039N LYS* 4.5 2.8 - - - +
1096N ILE* 3.6 9.2 - - - +
1097N PHE 3.7 1.1 - - - -
1098N ARG* 3.0 39.4 + - + +
1110N LYS* 5.6 2.7 - - + -
1111N SER* 1.3 75.4 - - - +
1113N TYR* 1.3 65.5 + - - +
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Residues in contact with TYR1113 (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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1023N ALA* 4.4 3.4 - - - -
1024N GLN* 3.4 29.3 + - + +
1026N ILE* 3.7 29.8 - - + -
1036N LEU* 4.0 21.5 - - + -
1037N LYS* 2.6 46.3 + - - +
1039N LYS* 3.8 14.9 + - - +
1051N TRP* 4.0 13.0 - + - -
1095N GLY 3.8 0.2 - - - +
1096N ILE* 3.3 8.3 - - - +
1097N PHE* 2.8 51.5 + - + +
1111N SER* 3.7 17.3 - - - -
1112N ASN* 1.3 79.9 + - - +
1114N ARG* 1.3 58.6 + - - +
1115N VAL* 3.9 6.2 + - + -
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Residues in contact with ARG1114 (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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1023N ALA* 4.1 16.7 - - + +
1024N GLN 2.9 11.0 + - - +
1025N ASN* 2.9 35.8 + - - +
1026N ILE 2.9 26.6 + - - +
1095N GLY 3.6 4.3 - - - +
1096N ILE* 4.8 7.9 - - + +
1113N TYR* 1.3 71.0 - - - +
1115N VAL* 1.3 60.6 + - - +
1116N ARG* 3.3 56.6 + - + +
1216N ARG* 6.1 0.2 - - - +
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Residues in contact with VAL1115 (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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1026N ILE* 3.5 19.1 - - + +
1028N ALA* 5.4 0.9 - - + -
1034N LEU* 4.1 27.1 - - + -
1036N LEU* 4.4 3.1 - - + -
1089N VAL* 5.9 0.4 - - + -
1093N ASP* 4.1 14.4 - - + +
1094N GLU* 3.3 3.1 - - - -
1095N GLY 2.8 21.2 + - - +
1097N PHE* 3.5 35.2 - - + -
1113N TYR* 4.4 9.2 - - + -
1114N ARG* 1.3 75.0 - - - +
1116N ARG* 1.3 90.5 + - - +
1117N VAL* 4.5 9.6 - - + -
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Residues in contact with ARG1116 (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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1025N ASN* 5.6 0.2 - - - +
1026N ILE 3.0 9.5 + - - +
1027N THR* 3.2 9.6 - - + -
1028N ALA 3.1 20.6 + - - -
1094N GLU* 3.4 22.7 - - - +
1095N GLY* 3.6 20.2 + - - +
1096N ILE* 6.0 0.4 - - - +
1114N ARG* 3.3 62.8 + - + +
1115N VAL* 1.3 89.9 + - - +
1117N VAL* 1.3 67.1 + - - +
1216N ARG* 3.6 26.5 - - - +
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Residues in contact with VAL1117 (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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1028N ALA* 3.0 14.1 - - + +
1030N ILE* 3.6 22.9 - - + -
1089N VAL* 3.9 20.2 - - + -
1090N GLY 3.8 13.2 - - - +
1091N ILE* 3.8 16.4 - - - -
1093N ASP* 5.2 0.9 - - + -
1094N GLU* 2.9 31.5 + - + +
1115N VAL* 4.5 10.5 - - + -
1116N ARG* 1.3 80.4 - - - +
1118N TYR* 1.3 66.5 + - - +
1150N TYR* 3.3 22.6 - - + -
1151N PRO* 4.1 5.5 - - - +
1216N ARG* 4.2 5.3 + - - -
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Residues in contact with TYR1118 (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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1027N THR* 4.6 5.8 - - - -
1028N ALA* 3.1 22.4 + - - -
1029N ARG* 3.3 43.6 + - + +
1030N ILE* 2.9 28.7 + - - -
1032N GLU* 5.4 0.2 + - - -
1117N VAL* 1.3 80.1 - - - +
1119N GLN* 1.3 64.6 + - - +
1120N ILE* 4.0 17.5 - - + +
1150N TYR* 3.1 15.9 - - - +
1151N PRO* 4.5 0.4 - - + -
1216N ARG* 3.7 57.1 + - + +
1217N HIS* 4.0 16.2 - + + -
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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