Contacts of the strand formed by residues 58 - 64 (chain B) in PDB entry 1RUO
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 GLU 58 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A PHE* 3.8 6.5 - - - -
50B LEU* 3.5 22.1 - - + +
51B ILE 3.2 13.2 - - - +
52B LYS* 3.1 39.1 - - + +
56B GLY 3.6 7.9 - - - +
57B LYS* 1.3 93.8 - - - +
59B MET* 1.3 66.3 + - - +
87B ARG* 4.3 9.2 + - - -
174B GLN* 4.0 32.7 + - + +
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Residues in contact with MET 59 (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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131A VAL* 3.9 23.6 - - + +
132A GLY* 5.6 0.7 - - - -
135A ALA* 4.0 16.4 - - + -
136A PHE* 4.1 13.7 - - + -
50B LEU* 3.0 30.6 - - - +
51B ILE* 2.8 24.0 + - + -
57B LYS* 6.1 0.7 - - - -
58B GLU* 1.3 79.1 - - - +
60B ILE* 1.3 74.5 + - - +
61B LEU* 3.8 2.5 - - + +
130B LYS* 3.9 16.8 - - - -
134B LEU* 5.2 4.0 - - + -
174B GLN* 3.7 9.2 - - - +
175B ILE 3.8 9.0 - - - +
176B VAL 3.7 7.2 - - - +
177B GLY* 3.3 39.3 - - - +
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Residues in contact with ILE 60 (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 ALA* 4.8 10.1 - - + -
49B VAL 4.7 0.7 - - - +
50B LEU* 4.1 9.9 - - + -
59B MET* 1.3 84.2 - - - +
61B LEU* 1.3 58.4 + - - +
62B SER 3.7 24.2 + - - +
63B TYR* 4.4 19.3 - - + +
130B LYS* 3.3 13.9 + - - -
171B GLU* 2.9 33.9 - - - +
174B GLN* 2.9 38.2 + - + +
175B ILE* 4.0 18.7 - - + +
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Residues in contact with LEU 61 (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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128A SER* 3.7 25.4 - - - +
131A VAL* 4.7 15.0 - - + -
49B VAL* 2.9 20.2 + - + +
50B LEU* 5.0 0.4 - - - -
51B ILE* 3.5 44.9 - - + -
59B MET* 3.8 1.9 - - + -
60B ILE* 1.3 73.1 - - - +
62B SER* 1.3 64.2 + - - +
84B ALA* 5.5 2.5 - - + -
127B THR* 4.9 4.7 + - + -
130B LYS* 4.4 15.1 - - + +
210B CMP 2.9 45.6 + - + +
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Residues in contact with SER 62 (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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49B VAL* 3.1 26.6 + - - -
60B ILE* 3.6 11.6 - - - +
61B LEU* 1.3 82.3 - - - +
63B TYR* 1.3 84.8 + - - +
64B LEU* 4.1 3.2 - - - +
123B ARG* 5.7 1.4 - - - +
126B VAL* 6.1 1.0 - - - +
210B CMP 3.1 27.2 - - - -
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Residues in contact with TYR 63 (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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46B SER* 6.3 0.9 - - - -
47B VAL 3.3 6.1 - - - +
48B ALA* 3.7 19.1 - - + -
49B VAL* 5.5 0.2 - - - -
60B ILE* 4.4 10.0 - - + +
62B SER* 1.3 88.7 + - - +
64B LEU* 1.3 82.1 + - - +
65B ASN* 4.9 3.8 - - - +
89B LYS* 2.9 48.8 + - + -
150B LEU* 5.1 10.3 - - + -
153B GLN* 3.6 40.4 + - - +
167B ILE* 4.0 12.8 - - + +
171B GLU* 2.9 20.1 + - - -
175B ILE* 4.4 20.0 - - + +
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Residues in contact with LEU 64 (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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42B ILE* 4.2 4.7 - - + -
46B SER* 3.5 0.7 - - - -
47B VAL* 2.9 43.1 + - + -
49B VAL* 3.9 26.5 - - + -
62B SER* 4.1 5.4 - - - +
63B TYR* 1.3 90.1 - - - +
65B ASN* 1.3 72.4 + - - +
68B ASP* 3.5 22.7 - - + +
69B PHE 4.5 3.8 - - - +
70B ILE* 5.4 4.5 - - + -
123B ARG* 3.1 42.6 - - + +
210B CMP 4.3 12.3 - - - +
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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