Contacts of the helix formed by residues 59 - 67 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C PRO* 1.3 76.1 - - - +
60C LEU* 1.3 55.3 + - - +
61C GLU* 3.7 8.9 + - - +
62C GLU* 2.8 31.6 + - - +
63C ILE* 2.8 35.3 + - - +
85D LEU 5.7 0.7 - - - -
86D LYS* 4.3 19.2 + - - +
88D ASN* 3.7 30.7 - - + +
185D PRO* 4.3 7.6 - - + -
244D ARG* 3.5 30.1 - - - +
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C THR* 1.3 72.1 - - - +
61C GLU* 1.3 62.7 + - - +
63C ILE* 3.4 10.9 + - + +
64C ILE* 3.0 47.2 + - + +
81C PHE* 4.1 21.1 - - + -
107C ALA* 4.3 10.8 - - + +
108C VAL* 4.3 14.4 - - + -
111C GLU* 4.2 22.7 - - + +
138C LEU* 4.2 32.5 - - + -
85D LEU* 4.8 15.7 - - + +
88D ASN* 2.9 20.6 + - - +
89D LEU 6.0 1.1 - - - +
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Residues in contact with GLU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C LYS* 4.6 4.7 + - - -
59C THR* 3.3 8.5 + - - +
60C LEU* 1.3 77.9 - - - +
62C GLU* 1.3 60.1 + - + +
64C ILE* 3.3 2.9 + - - +
65C LEU* 2.9 45.1 + - + +
77C PRO* 3.6 25.6 - - + +
78C LYS 5.2 0.3 + - - -
81C PHE* 3.9 18.8 - - + -
219C HIS* 6.1 0.4 - - - -
82D TYR* 2.6 36.9 + - - -
85D LEU 5.3 0.6 + - - -
86D LYS* 2.7 33.5 + - + +
211D GLU* 4.2 3.8 - - - +
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Residues in contact with GLU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 3.2 39.5 - - + +
18C LYS* 2.7 35.7 + - + +
20C LEU* 4.9 1.6 - - - +
58C PRO* 3.4 11.5 - - + +
59C THR* 2.8 42.7 + - - +
61C GLU* 1.3 77.9 - - - +
63C ILE* 1.3 60.4 + - - +
65C LEU* 4.5 4.7 - - + +
66C LEU* 2.9 37.8 + - + +
67C GLY 3.7 0.2 + - - -
86D LYS* 4.9 1.2 + - - -
209D ASN* 3.4 7.1 + - - -
211D GLU* 4.4 0.9 - - - +
244D ARG* 3.6 10.9 + - - -
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Residues in contact with ILE 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C LEU* 5.2 1.3 - - - -
58C PRO* 3.9 31.2 - - + +
59C THR 2.8 26.6 + - - +
60C LEU* 3.6 11.2 - - + +
61C GLU 3.3 0.2 - - - -
62C GLU* 1.3 73.0 - - - +
64C ILE* 1.3 57.8 + - + +
67C GLY* 2.8 27.4 + - - +
68C PHE* 3.0 35.7 + - + -
136C PHE* 3.5 44.6 - - + +
138C LEU* 4.5 10.3 - - + -
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Residues in contact with ILE 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LEU* 3.0 37.6 + - + +
61C GLU 3.7 3.6 - - - +
63C ILE* 1.3 77.9 - - + +
65C LEU* 1.3 63.4 + - - +
68C PHE* 3.5 32.3 + - + +
70C ARG* 4.5 1.6 + - - -
74C ILE* 4.4 13.4 - - + +
75C ILE 4.5 0.7 - - - +
77C PRO* 4.0 30.1 - - + -
80C SER* 5.0 0.4 - - - +
81C PHE* 4.6 1.1 - - + -
104C ALA* 3.7 43.3 - - + +
107C ALA* 4.3 11.0 - - + -
108C VAL* 3.7 20.9 - - + -
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Residues in contact with LEU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C GLU* 2.9 42.7 + - + +
62C GLU* 4.3 2.7 - - - +
64C ILE* 1.3 78.2 - - - +
66C LEU* 1.3 72.5 + - + +
68C PHE 5.2 1.1 - - - +
70C ARG* 2.9 31.3 + - - +
74C ILE* 4.6 2.9 - - + -
76C TYR* 3.6 31.0 - - + -
77C PRO* 3.8 18.2 - - + -
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 3.7 28.9 - - + -
18C LYS* 4.0 32.3 - - + +
19C PHE* 5.7 0.2 - - - -
20C LEU* 3.8 27.8 - - + +
62C GLU* 2.9 17.5 + - + +
65C LEU* 1.3 88.4 - - + +
67C GLY* 1.3 60.9 + - - +
68C PHE 3.9 1.6 - - - -
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Residues in contact with GLY 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C LEU* 3.4 19.7 - - - -
62C GLU 3.7 1.4 + - - -
63C ILE 2.8 14.6 + - - -
66C LEU* 1.3 81.1 - - - +
68C PHE* 1.3 61.4 + - - +
69C GLU* 3.5 0.3 + - - -
135C LYS* 3.5 23.0 + - - -
136C PHE* 3.7 14.5 - - - -
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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