Contacts of the strand formed by residues 59 - 66 (chain B) in PDB entry 4I0A
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 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A PHE* 4.2 2.2 - - - -
51B LEU* 4.1 11.5 - - + +
52B ILE 3.4 6.1 - - - +
53B LYS* 4.0 21.9 + - + -
57B GLY 3.7 14.2 - - - +
58B LYS* 1.3 76.3 - - - +
60B MET* 1.3 61.0 + - - +
88B ARG* 3.0 31.1 + - - -
174B GLY 3.8 1.7 - - - +
175B GLN* 3.0 43.5 - - + +
178B GLY* 3.6 16.8 - - - -
179B CYS 4.5 1.0 + - - +
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Residues in contact with MET 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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132A ALA 4.5 5.4 - - - +
133A GLY* 5.2 1.3 - - - -
136A ALA* 3.5 19.3 - - + -
137A PHE* 3.7 16.4 - - + -
51B LEU* 3.4 3.1 - - - -
52B ILE* 2.8 41.1 + - + +
59B GLU* 1.3 75.8 - - - +
61B ILE* 1.3 70.5 + - - +
62B LEU* 3.5 8.4 + - + -
131B LYS* 3.3 14.8 - - - +
135B LEU* 3.5 32.3 - - + -
175B GLN 3.2 10.5 - - - +
176B ILE 3.1 20.9 - - - +
177B VAL* 3.4 20.9 - - - +
178B GLY* 3.8 4.7 - - - +
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Residues in contact with ILE 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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49B ALA* 3.8 12.3 - - + -
50B VAL 3.3 5.6 - - - +
51B LEU* 3.0 26.9 - - + -
60B MET* 1.3 73.5 - - - +
62B LEU* 1.3 60.7 + - - +
63B SER* 3.6 29.2 - - - +
64B TYR* 3.4 37.5 - - + +
90B LYS* 6.1 0.2 - - - +
131B LYS* 3.2 24.6 + - - -
175B GLN* 2.8 45.4 + - + +
176B ILE* 4.9 7.1 - - + +
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Residues in contact with LEU 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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129A SER* 3.8 29.8 - - - +
132A ALA* 4.1 22.4 - - + -
50B VAL* 2.7 20.6 + - + +
52B ILE* 3.6 50.3 - - + +
60B MET* 3.5 5.1 + - - -
61B ILE* 1.3 74.5 - - - +
63B SER* 1.3 62.2 + - - +
85B ALA* 4.7 1.3 - - + -
127B VAL* 5.2 7.3 - - - +
128B THR* 4.6 10.5 + - + +
131B LYS* 4.3 20.4 - - + +
301B CMP 3.9 28.1 + - + +
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Residues in contact with SER 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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49B ALA* 3.6 1.4 - - - -
50B VAL* 2.7 36.7 + - - +
61B ILE* 3.4 10.8 - - - +
62B LEU* 1.3 84.1 - - - +
64B TYR* 1.3 78.7 + - - +
65B LEU* 3.8 8.2 - - - +
124B ARG* 5.7 0.7 - - - +
127B VAL* 5.6 6.4 - - - +
301B CMP 3.6 28.3 - - - -
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Residues in contact with TYR 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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47B SER* 5.8 2.7 - - - -
48B VAL 3.3 13.2 - - - +
49B ALA* 3.9 19.3 - - + -
61B ILE* 3.4 25.8 - - + +
63B SER* 1.3 87.5 + - - +
65B LEU* 1.3 64.1 + - - +
66B ASN* 4.3 16.9 + - - +
69B ASP* 4.9 0.2 - - - +
90B LYS* 3.6 42.1 + - + -
168B ILE* 6.0 1.0 - - - +
172B GLU* 4.5 10.0 + - - +
175B GLN* 4.7 4.2 + - - -
176B ILE* 5.4 15.4 - - + +
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Residues in contact with LEU 65 (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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43B ILE* 3.8 4.8 - - + +
47B SER* 3.3 3.8 - - - -
48B VAL* 2.9 42.6 + - + +
50B VAL* 3.6 28.5 - - + -
63B SER* 3.8 10.3 - - - +
64B TYR* 1.3 81.7 - - - +
66B ASN* 1.3 64.7 + - - +
69B ASP* 3.4 19.7 - - + +
70B PHE 4.1 3.1 - - - +
71B ILE* 4.0 19.3 - - + -
124B ARG* 3.8 42.8 - - + +
301B CMP 4.1 5.8 - - + +
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Residues in contact with ASN 66 (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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43B ILE* 3.6 8.1 - - - +
46B GLY 3.6 9.2 - - - +
47B SER* 2.4 29.0 + - - +
64B TYR* 4.3 13.1 + - - +
65B LEU* 1.3 81.3 + - - +
67B GLN* 1.3 71.9 + - + +
69B ASP* 2.7 34.6 + - - +
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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