Contacts of the strand formed by residues 108 - 113 (chain 1) in PDB entry 1ILR
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 THR 108 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181 VAL* 3.9 19.5 - - + -
1041 ASP* 3.5 4.9 - - - +
1051 SER* 3.2 35.8 + - - -
1061 GLY 3.4 1.5 - - - +
1071 PRO* 1.3 89.4 - - + +
1091 THR* 1.3 67.6 + - - +
1451 LYS* 3.8 25.5 - - + +
1461 PHE 3.2 10.8 - - - +
1471 TYR* 3.8 27.4 - - + +
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Residues in contact with THR 109 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021 ARG* 3.5 32.0 + - + +
1031 SER 3.4 4.5 - - - +
1041 ASP* 2.8 24.2 + - - +
1071 PRO 5.2 0.3 + - - -
1081 THR* 1.3 76.6 - - - +
1101 SER* 1.3 70.1 + - - +
1111 PHE* 3.8 17.7 - - + -
1451 LYS* 4.7 0.7 - - - -
1461 PHE* 2.7 42.5 + - - -
1481 PHE* 3.6 21.5 + - + +
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Residues in contact with SER 110 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011 ILE 3.5 0.7 - - - +
1021 ARG* 3.4 4.3 - - - -
1031 SER* 2.8 48.1 + - - -
1091 THR* 1.3 74.2 - - - +
1111 PHE* 1.3 64.3 + - - +
1201 PHE* 4.3 17.5 - - - -
1441 THR* 3.0 23.2 + - - -
1451 LYS* 3.2 28.7 + - - +
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Residues in contact with PHE 111 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151 ILE* 4.0 19.1 - - + -
561 LEU* 4.1 16.2 - - + -
581 LEU* 4.1 22.0 - - + -
1001 PHE* 4.3 13.5 - - + -
1011 ILE 3.3 4.5 - - - +
1021 ARG* 4.6 4.9 - - + -
1091 THR* 3.8 19.5 - - + -
1101 SER* 1.3 77.9 - - - +
1121 GLU* 1.3 61.0 + - - +
1201 PHE* 3.2 7.4 - - - +
1211 LEU* 2.9 57.5 + - + +
1441 THR 4.9 0.6 + - - -
1461 PHE* 4.2 16.6 - + + -
1481 PHE* 3.6 52.9 - + - -
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Residues in contact with GLU 112 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001 PHE* 3.3 4.8 - - - -
1011 ILE* 2.6 57.9 + - + +
1101 SER 4.2 0.4 - - - -
1111 PHE* 1.3 73.9 - - - +
1131 SER* 1.3 73.7 + - - +
1171 PRO* 3.6 7.0 - - - +
1181 GLY* 2.6 29.3 + - - +
1191 TRP 3.3 12.1 - - - +
1201 PHE* 3.8 29.1 - - + -
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Residues in contact with SER 113 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691 CYS* 3.3 25.2 - - - +
971 ARG 5.1 0.7 + - - -
991 ALA 4.0 1.7 + - - -
1001 PHE* 3.8 20.8 - - - -
1011 ILE* 3.9 1.9 - - - +
1111 PHE 4.1 0.2 + - - -
1121 GLU* 1.3 76.2 - - - +
1141 ALA* 1.3 62.7 + - - +
1151 ALA* 3.4 2.3 + - - +
1161 CYS* 2.9 34.7 + - - -
1171 PRO* 3.5 21.1 - - - +
1191 TRP* 2.8 17.0 + - - -
1331 LEU* 4.7 2.2 - - - -
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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