Contacts of the strand formed by residues 119 - 123 (chain A) in PDB entry 1D5R
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 VAL 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A PRO 4.2 4.7 - - - +
31A ASN* 3.4 22.2 - - + +
33A ILE* 4.3 19.1 - - + -
57A LEU* 6.0 0.9 - - + -
61A HIS* 3.3 40.6 - - + +
64A HIS 3.1 11.4 + - - +
65A TYR* 3.3 7.6 - - + -
66A LYS 3.1 14.6 + - - -
111A TRP* 2.9 18.5 + - - +
112A LEU* 4.1 0.7 - - - -
118A HIS* 1.3 98.7 - - + +
120A ALA* 1.3 66.4 + - - +
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Residues in contact with ALA 120 (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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31A ASN 2.8 13.5 + - - +
32A ILE* 3.6 3.3 - - + -
33A ILE* 2.7 34.9 + - - +
66A LYS 3.5 9.6 - - - +
68A TYR* 4.0 14.8 - - + -
108A LEU* 4.0 18.6 - - + -
111A TRP* 4.5 2.9 - - + -
112A LEU* 4.2 3.1 - - + -
119A VAL* 1.3 79.9 - - - +
121A ALA* 1.3 55.9 + - - +
122A ILE* 3.7 15.9 - - + +
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Residues in contact with ALA 121 (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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33A ILE* 3.3 17.0 - - + -
35A MET* 3.8 20.9 - - - -
57A LEU* 4.7 12.3 - - + -
65A TYR* 6.0 1.5 - - + +
66A LYS 3.2 8.3 + - - +
67A ILE* 3.4 31.1 - - + +
68A TYR 3.1 21.7 + - - -
119A VAL* 6.1 0.2 - - + -
120A ALA* 1.3 71.2 - - - +
122A ILE* 1.3 63.0 + - - +
123A HIS* 4.9 0.2 - - - -
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Residues in contact with ILE 122 (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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32A ILE* 4.4 14.8 - - + -
33A ILE 2.8 13.9 + - - +
34A ALA* 3.5 3.8 - - - -
35A MET* 2.9 24.1 + - - +
68A TYR* 3.7 22.4 - - + +
70A LEU* 3.6 31.9 - - + -
104A PHE* 4.1 18.2 - - + -
108A LEU* 4.7 8.1 - - + -
120A ALA* 3.7 28.3 - - + +
121A ALA* 1.3 76.5 - - - +
123A HIS* 1.3 65.7 + - - +
131A THR* 3.6 20.5 - - + +
134A MET* 5.2 0.4 - - + -
135A ILE* 4.5 9.6 - - + -
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Residues in contact with HIS 123 (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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35A MET* 3.3 29.8 - - + +
36A GLY 3.5 8.1 - - - +
37A PHE* 3.7 16.6 - + - -
38A PRO* 3.8 12.9 - - + +
67A ILE* 3.7 15.5 - - + -
68A TYR 3.1 19.2 + - - +
69A ASN* 2.8 35.1 + - - +
70A LEU* 3.1 26.1 + - - +
76A TYR* 2.9 28.0 + + - -
122A ILE* 1.3 77.4 - - - +
124A CYS* 1.3 75.0 + - - +
131A THR* 3.6 6.7 - - - -
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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