Contacts of the strand formed by residues 107 - 113 (chain 3) in PDB entry 5LN3
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 PRO 107 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513 ILE* 4.4 9.2 - - + -
523 GLY 3.3 10.1 - - - +
533 LEU* 3.9 21.1 - - + -
913 VAL* 3.8 28.9 - - + -
953 LEU* 4.0 13.9 - - + -
1053 THR* 3.8 7.9 - - + +
1063 GLU* 1.3 92.2 - - - +
1083 VAL* 1.3 72.7 + - - +
1233 SER* 4.0 0.2 + - - -
1243 LEU* 3.2 40.4 + - + +
1253 ASP 4.9 0.2 - - - +
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Residues in contact with VAL 108 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113 VAL* 4.4 19.1 - - + +
123 MET 6.1 0.9 - - - -
133 ALA* 5.8 4.9 - - + -
223 ILE* 5.0 7.3 - - + +
503 TYR 4.2 0.3 - - - +
513 ILE* 3.6 4.2 - - - +
523 GLY* 2.8 46.5 + - - +
1063 GLU* 6.0 0.4 - - + -
1073 PRO* 1.3 82.0 - - - +
1093 ILE* 1.4 64.6 + - - +
1103 ALA* 6.5 0.2 - - + -
1223 CYS 3.4 6.5 - - - +
1233 SER* 3.4 20.4 - - - +
1243 LEU* 5.7 0.2 - - - -
1373 VAL* 3.5 24.2 - - + -
1383 VAL 3.9 10.1 - - - +
1393 SER* 4.0 14.6 - - - +
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Residues in contact with ILE 109 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493 LEU* 6.0 2.9 - - + -
503 TYR 3.8 7.0 - - - +
513 ILE* 3.8 20.4 - - + -
843 PRO* 4.5 7.6 - - + +
873 LEU* 3.9 22.7 - - + +
883 MET* 3.5 39.5 - - + +
913 VAL* 4.6 1.6 - - + -
1083 VAL* 1.4 80.0 - - - +
1103 ALA* 1.4 70.6 - - - +
1203 PHE* 3.8 23.8 - - + -
1213 ILE* 3.3 7.8 - - - +
1223 CYS* 2.7 36.2 + - + +
1243 LEU* 4.1 16.6 - - + -
1373 VAL* 5.0 0.7 - - - +
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Residues in contact with ALA 110 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133 ALA* 4.5 15.3 - - + -
203 VAL* 5.6 5.8 - - + -
213 ALA 5.3 2.5 - - - +
223 ILE* 4.5 20.2 - - + -
493 LEU* 3.9 2.2 - - - +
503 TYR* 2.9 36.8 + - + +
1083 VAL* 6.5 0.2 - - + -
1093 ILE* 1.4 66.8 - - - +
1113 GLY* 1.3 57.7 + - - +
1203 PHE* 3.5 8.3 - - - -
1213 ILE* 3.7 11.9 - - + -
1903 ILE* 6.4 0.7 - - + -
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Residues in contact with GLY 111 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203 VAL* 4.1 15.0 - - - +
483 ARG 3.3 16.4 - - - -
493 LEU* 3.9 10.1 - - - -
503 TYR* 5.6 1.1 - - - -
843 PRO* 6.1 0.2 - - - -
1103 ALA* 1.3 76.5 - - - +
1123 LEU* 1.3 62.1 + - - +
1133 ASP 4.1 0.4 - - - -
1193 PRO* 4.0 0.3 - - - +
1203 PHE* 2.7 34.7 + - - +
1213 ILE* 5.0 0.2 - - - +
1903 ILE* 5.6 0.4 - - - -
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Residues in contact with LEU 112 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183 ASN* 4.2 4.9 - - - -
193 CYS* 3.5 40.8 - - - +
203 VAL* 4.1 10.4 - - + +
483 ARG* 3.7 20.0 + - - +
493 LEU* 5.0 0.9 - - - -
1113 GLY* 1.3 75.5 - - - -
1133 ASP* 1.4 87.7 + - - +
1143 PRO* 3.4 10.0 - - - +
1173 PHE* 4.2 5.4 - - - -
1183 LYS 3.5 22.2 - - - +
1193 PRO* 3.7 15.9 - - + -
1903 ILE* 4.7 9.5 - - + +
1923 LYS* 4.1 34.9 - - + +
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Residues in contact with ASP 113 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483 ARG* 5.2 0.9 - - - -
493 LEU* 5.3 2.4 - - - +
833 LYS* 4.8 2.8 - - - +
843 PRO* 3.5 33.7 - - + +
1113 GLY 4.1 1.4 + - - -
1123 LEU* 1.4 71.9 - - - +
1143 PRO* 1.3 62.0 - - - +
1153 LYS* 3.1 31.1 + - - +
1163 THR* 2.9 35.3 + - - +
1173 PHE* 2.8 23.7 + - - -
1183 LYS* 2.9 22.8 + - + +
1203 PHE* 5.2 1.9 - - + +
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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