Contacts of the strand formed by residues 113 - 121 (chain B) in PDB entry 3ULA
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 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B ILE* 3.2 7.3 - - + +
65B TYR* 3.2 36.8 + - + +
67B PRO* 3.7 21.8 - - + -
71B LEU* 4.0 7.2 - - + -
104B PHE* 3.9 17.9 - - + -
107B ALA* 3.6 31.0 - - + -
111B GLU 3.5 0.9 + - - +
112B THR* 1.3 76.4 - - - +
114B ASN* 1.3 56.7 + - - +
115B THR* 3.6 24.7 - - + -
401C E55 4.5 13.7 - - + -
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Residues in contact with ASN 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A HIS* 6.0 0.2 - - - -
62B HIS* 3.4 23.6 - - - -
63B ILE 3.8 3.3 - - - +
64B PHE* 3.8 29.6 - - + +
112B THR* 3.6 10.7 + - + -
113B VAL* 1.3 72.7 - - - +
115B THR* 1.3 56.6 + - - +
116B THR* 5.3 0.2 + - - -
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Residues in contact with THR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B HIS* 3.0 27.4 + - - -
63B ILE* 3.1 25.7 + - + +
103B SER* 5.4 5.1 + - - -
104B PHE* 3.6 26.4 - - + -
113B VAL* 3.6 24.9 - - + -
114B ASN* 1.3 74.5 - - - +
116B THR* 1.3 90.1 + - - +
117B ILE* 3.6 10.1 - - + +
401C E55 5.2 2.5 - - + -
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Residues in contact with THR 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LEU* 4.2 31.2 - - + -
61B LEU 3.6 11.4 - - - +
62B HIS* 3.2 26.8 + - + +
115B THR* 1.3 96.4 + - - +
117B ILE* 1.3 66.6 + - - +
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LEU* 3.4 6.2 - - - -
61B LEU* 2.8 48.8 + - + +
102B TYR* 3.3 44.4 - - + +
104B PHE* 3.4 22.7 - - + -
115B THR* 3.6 9.0 - - + +
116B THR* 1.3 81.6 - - - +
118B SER* 1.3 79.0 + - - +
401C E55 3.9 36.6 - - + -
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Residues in contact with SER 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLY 3.5 7.9 - - - -
60B LEU* 4.1 12.9 - - - +
102B TYR* 5.1 0.5 + - - -
117B ILE* 1.3 93.1 - - - +
119B PHE* 1.3 60.8 + - - +
401C E55 3.6 7.3 - - - +
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Residues in contact with PHE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B VAL* 3.8 26.2 - - + -
50B PRO 4.0 4.7 - - - -
52B ILE* 4.1 15.7 - - + -
57B SER* 4.1 7.0 - - - -
58B LYS* 3.3 12.7 - - - +
59B GLY* 2.8 63.7 + - - +
60B LEU 3.0 7.4 - - - -
61B LEU* 3.1 36.6 - - + -
118B SER* 1.3 76.9 - - - +
120B SER* 1.3 63.5 + - - +
121B PHE 4.2 3.8 - - - -
401C E55 3.5 44.6 - - + +
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Residues in contact with SER 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B SER 5.4 0.2 - - - -
58B LYS* 3.9 15.3 - - - +
119B PHE* 1.3 76.0 - - - +
121B PHE* 1.3 61.5 + - - +
122B LYS* 3.7 8.6 + - - +
294C LYS* 3.6 22.8 + - - -
401C E55 2.7 37.7 + - - +
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Residues in contact with PHE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ILE* 3.4 46.4 - - + -
53B GLU 3.9 11.9 - - - -
54B LEU* 4.0 14.1 - - + -
56B GLY* 3.3 1.6 - - - -
57B SER 2.9 44.5 + - - +
119B PHE* 4.2 1.6 - - + -
120B SER* 1.3 70.7 - - - +
122B LYS* 1.3 71.6 + - - +
124B ILE* 3.9 20.9 - - + -
401C E55 3.1 88.6 - - + -
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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