Contacts of the helix formed by residues 57 - 65 (chain B) in PDB entry 4V1M
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 TYR 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B GLN* 3.1 42.5 + - - +
56B ASP* 1.3 102.3 - - + +
58B THR* 1.3 68.5 + - - +
59B LEU 2.9 3.8 + - - -
60B GLN* 2.9 16.8 + - - +
61B ASP* 3.2 20.0 + - - +
177B LYS* 5.8 2.7 + - - -
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Residues in contact with THR 58 (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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53B GLN* 3.3 21.4 + - - +
54B PHE* 3.4 36.3 - - + +
57B TYR* 1.3 76.4 - - - +
59B LEU* 1.3 60.9 + - - +
61B ASP* 3.4 3.3 + - - +
62B ILE* 3.1 27.7 + - + +
246B LYS* 4.1 28.1 + - - +
410B GLY 6.0 0.4 - - - -
414B ALA* 3.7 19.7 - - + -
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Residues in contact with LEU 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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54B PHE* 2.9 43.9 + - + +
55B VAL* 3.8 23.8 - - + +
57B TYR 2.9 2.8 + - - -
58B THR* 1.3 73.0 - - - +
60B GLN* 1.3 64.0 + - - +
62B ILE* 3.3 6.2 + - - +
63B ILE* 3.3 21.1 + - - +
95B ILE* 3.7 29.5 - - + +
97B VAL* 5.2 5.4 - - + -
128B LEU* 4.0 20.6 - - + -
170B LEU* 4.2 11.9 - - + -
417B PHE* 3.7 32.1 - - + -
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Residues in contact with GLN 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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55B VAL 5.2 0.6 + - - -
56B ASP 5.1 6.3 - - - +
57B TYR* 2.9 10.9 + - - +
59B LEU* 1.3 80.4 - - - +
61B ASP* 1.3 67.0 + - - +
63B ILE* 3.1 32.7 + - - +
64B CYS* 3.2 24.1 + - - -
93B GLY 3.2 24.2 + - - -
94B LYS* 3.6 9.5 - - - +
95B ILE* 3.0 35.7 + - + +
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Residues in contact with ASP 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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57B TYR* 3.2 20.7 + - - +
58B THR* 3.9 6.2 - - - +
59B LEU 3.3 0.6 - - - -
60B GLN* 1.3 81.4 - - - +
62B ILE* 1.3 61.0 + - - +
64B CYS* 3.7 6.9 - - - +
65B GLU* 3.2 26.0 + - - +
246B LYS* 4.1 23.8 + - + +
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Residues in contact with ILE 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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54B PHE* 4.3 3.1 - - + -
58B THR* 3.1 22.7 + - + +
59B LEU* 3.7 4.9 - - - +
60B GLN 3.2 0.2 - - - -
61B ASP* 1.3 76.2 - - - +
63B ILE* 1.3 62.5 + - - +
64B CYS 3.2 1.5 + - - -
65B GLU* 3.6 19.9 + - - +
66B ASP* 4.2 0.2 - - - +
246B LYS* 4.6 3.4 - - + -
414B ALA* 3.5 44.0 - - + +
417B PHE* 3.5 34.8 - - + +
418B LYS* 3.8 35.4 - - + -
421B PHE* 3.7 18.5 - - + -
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Residues in contact with ILE 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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59B LEU 3.3 7.2 + - - +
60B GLN* 3.1 35.2 + - - +
62B ILE* 1.3 80.2 - - - +
64B CYS* 1.3 58.6 + - - +
67B SER* 3.2 22.1 - - - -
92B PHE* 4.1 13.6 - - + +
93B GLY 3.7 12.3 - - - +
95B ILE* 4.4 13.5 - - + -
130B VAL* 4.2 21.3 - - + -
167B ILE* 4.6 5.8 - - + -
417B PHE* 3.9 24.0 - - + -
421B PHE* 3.4 40.9 - - + -
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Residues in contact with CYS 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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60B GLN* 3.2 39.5 + - - +
61B ASP* 3.4 7.6 + - - +
62B ILE 3.2 0.6 - - - -
63B ILE* 1.3 83.6 - - - +
65B GLU* 1.3 66.9 + - - +
67B SER* 3.4 16.4 + - - -
92B PHE 4.4 10.8 - - - -
93B GLY* 4.7 1.3 - - - -
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Residues in contact with GLU 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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61B ASP 3.2 12.6 + - - +
62B ILE* 3.6 23.3 - - - +
63B ILE 3.7 0.2 - - - -
64B CYS* 1.3 81.3 - - - +
66B ASP* 1.3 78.0 + - - +
67B SER* 4.1 0.9 + - - -
246B LYS* 4.9 3.8 - - - +
247B GLY* 3.1 32.3 - - - -
248B SER 4.1 3.1 + - - -
418B LYS* 3.5 33.3 - - - +
422B LYS* 4.1 9.7 + - - -
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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