Contacts of the helix formed by residues 59 - 67 (chain A) in PDB entry 2YVL
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 THR 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A PRO* 1.3 76.4 - - - +
60A LEU* 1.3 65.5 + - - +
61A GLU* 3.6 8.5 + - - +
62A GLU* 2.8 32.7 + - - +
63A ILE* 2.9 24.8 + - - +
85B LEU 5.6 0.2 - - - -
86B LYS* 4.3 15.6 + - - +
88B ASN* 3.7 29.4 - - + +
185B PRO* 4.3 9.4 - - + -
244B ARG* 3.6 29.8 - - - +
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Residues in contact with LEU 60 (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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59A THR* 1.3 71.5 - - - +
61A GLU* 1.3 63.4 + - - +
63A ILE* 3.4 9.9 + - + +
64A ILE* 3.1 47.0 + - + +
81A PHE* 3.9 22.7 - - + -
107A ALA* 4.3 13.5 - - + +
108A VAL* 4.4 8.1 - - + -
111A GLU* 4.1 32.1 - - + +
138A LEU* 4.4 16.6 - - + -
85B LEU* 4.2 24.5 - - + +
88B ASN* 2.8 21.2 + - - +
89B LEU 5.9 1.1 - - - +
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LYS* 4.6 4.5 + - - -
59A THR* 3.2 8.5 + - - +
60A LEU* 1.3 79.8 - - - +
62A GLU* 1.3 59.9 + - - +
64A ILE* 3.6 2.1 + - - +
65A LEU* 3.0 44.8 + - + +
77A PRO* 3.7 24.3 - - + +
78A LYS 5.2 0.3 + - - -
81A PHE* 3.8 20.6 - - + -
219A HIS* 6.1 0.7 - - - -
82B TYR* 2.6 38.0 + - - -
85B LEU 5.3 0.6 + - - -
86B LYS* 2.8 31.2 + - + +
211B GLU* 4.1 4.5 - - - +
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Residues in contact with GLU 62 (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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11A LEU* 3.5 30.8 - - + +
18A LYS* 2.8 35.5 + - + +
20A LEU* 4.8 2.6 - - - +
58A PRO* 3.3 12.3 - - + +
59A THR* 2.8 41.9 + - - +
61A GLU* 1.3 79.4 - - + +
63A ILE* 1.3 60.9 + - - +
65A LEU* 4.5 5.2 - - + +
66A LEU* 2.9 37.4 + - + +
67A GLY 3.7 0.5 + - - -
86B LYS* 5.1 1.5 + - - +
209B ASN* 3.2 18.5 + - - -
211B GLU* 4.6 0.5 - - - +
244B ARG* 3.5 9.4 + - - -
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Residues in contact with ILE 63 (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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20A LEU* 5.1 1.3 - - - -
58A PRO* 3.9 26.7 - - + +
59A THR 2.9 26.7 + - - +
60A LEU* 3.6 9.6 - - + +
62A GLU* 1.3 75.8 - - - +
64A ILE* 1.3 58.5 + - + +
67A GLY* 2.8 27.7 + - - +
68A PHE* 3.0 27.9 + - + -
136A PHE* 3.5 51.4 - - + +
138A LEU* 4.4 11.9 - - + -
88B ASN* 6.1 0.2 - - - +
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Residues in contact with ILE 64 (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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60A LEU* 3.1 33.3 + - + +
61A GLU 3.9 3.6 - - - +
63A ILE* 1.3 77.3 - - + +
65A LEU* 1.3 63.4 + - - +
66A LEU 3.6 0.2 + - - -
68A PHE* 3.4 31.4 + - + +
70A ARG* 4.6 1.2 + - - -
74A ILE* 4.4 12.8 - - + +
75A ILE 4.4 0.7 - - - +
77A PRO* 4.1 27.8 - - + -
80A SER* 5.0 0.7 - - - +
81A PHE* 4.7 1.1 - - + -
104A ALA* 3.6 45.3 - - + +
107A ALA* 4.1 12.1 - - + -
108A VAL* 3.8 21.1 - - + -
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Residues in contact with LEU 65 (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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61A GLU* 3.0 40.9 + - + +
62A GLU* 4.2 3.8 - - + +
64A ILE* 1.3 79.5 - - + +
66A LEU* 1.3 72.8 + - + +
68A PHE 5.4 1.1 - - - +
70A ARG* 3.0 28.8 + - - +
74A ILE* 4.8 0.4 - - + -
76A TYR* 3.9 21.1 - - + -
77A PRO* 3.4 31.9 - - + -
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Residues in contact with LEU 66 (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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11A LEU* 3.9 28.3 - - + -
18A LYS* 4.0 34.3 - - + +
19A PHE* 5.6 0.2 - - - -
20A LEU* 3.8 26.3 - - + +
62A GLU* 2.9 16.4 + - + +
65A LEU* 1.3 88.3 - - + +
67A GLY* 1.3 60.0 + - - +
68A PHE 3.9 2.0 - - - +
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Residues in contact with GLY 67 (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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9A TYR* 6.1 0.2 - - - -
20A LEU* 3.5 19.3 - - - -
62A GLU 3.7 1.2 + - - -
63A ILE 2.8 14.5 + - - -
66A LEU* 1.3 80.4 - - - +
68A PHE* 1.3 61.7 + - - +
69A GLU 3.4 2.4 + - - -
132A ASN* 4.5 1.2 - - - +
135A LYS* 4.4 10.2 + - - -
136A PHE* 3.8 20.7 - - - -
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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