Contacts of the helix formed by residues 59 - 67 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C LEU 5.7 0.4 - - - -
86C LYS* 4.4 13.6 + - - +
88C ASN* 3.8 31.4 - - + +
185C PRO* 4.2 10.1 - - + -
244C ARG* 3.4 29.4 - - - +
58D PRO* 1.3 75.6 - - - +
60D LEU* 1.3 55.0 + - - +
61D GLU* 3.6 8.3 + - - +
62D GLU* 2.8 33.0 + - - +
63D ILE* 2.8 35.7 + - - +
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Residues in contact with LEU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C LEU* 4.5 20.6 - - + +
88C ASN* 3.0 24.1 - - - +
89C LEU 6.0 0.9 - - - +
59D THR* 1.3 70.1 - - - +
61D GLU* 1.3 62.5 + - - +
63D ILE* 3.5 9.9 + - + +
64D ILE* 3.1 48.0 + - + +
81D PHE* 4.0 20.4 - - + -
107D ALA* 4.3 10.8 - - + +
108D VAL* 4.4 8.5 - - + -
111D GLU* 4.2 26.2 - - + -
138D LEU* 4.1 28.5 - - + -
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Residues in contact with GLU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TYR* 2.5 36.3 + - - -
85C LEU 5.3 0.6 + - - -
86C LYS* 2.7 34.2 + - + -
211C GLU* 4.2 2.8 - - - +
18D LYS* 4.5 6.1 + - - -
59D THR* 3.2 8.0 + - - +
60D LEU* 1.3 78.7 - - - +
62D GLU* 1.3 60.8 + - - +
64D ILE* 3.4 1.8 + - - +
65D LEU* 3.0 43.6 + - + +
77D PRO* 3.7 25.8 - - + +
78D LYS 5.3 0.2 + - - -
81D PHE* 3.8 19.3 - - + -
217D HIS* 5.6 0.3 - - - -
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Residues in contact with GLU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C LYS* 5.2 1.0 + - - -
209C ASN* 3.2 17.7 - - - +
211C GLU* 4.6 1.0 - - - +
244C ARG* 3.1 16.0 + - - -
11D LEU* 3.2 29.8 - - + +
18D LYS* 2.9 33.2 + - + +
20D LEU* 4.6 1.1 - - - +
58D PRO* 3.4 8.9 - - + +
59D THR* 2.8 36.7 + - - +
61D GLU* 1.3 76.7 - - - +
63D ILE* 1.3 61.0 + - - +
65D LEU* 4.6 4.0 - - - +
66D LEU* 2.9 38.7 + - + +
67D GLY 3.7 0.2 + - - -
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Residues in contact with ILE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D LEU* 4.9 1.6 - - - -
58D PRO* 3.8 31.6 - - + +
59D THR 2.8 27.7 + - - +
60D LEU* 3.7 10.5 - - + +
61D GLU 3.3 0.2 - - - -
62D GLU* 1.3 72.6 - - - +
64D ILE* 1.3 58.7 + - + +
67D GLY* 2.7 33.9 + - - +
68D PHE* 3.0 23.6 + - + -
136D PHE* 3.6 49.6 - - + +
138D LEU* 4.6 12.1 - - + -
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Residues in contact with ILE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D LEU* 3.1 36.0 + - + +
61D GLU 3.8 3.4 - - - +
63D ILE* 1.3 79.1 - - + +
65D LEU* 1.3 62.7 + - - +
66D LEU 3.5 0.2 + - - -
68D PHE* 3.6 32.5 + - + +
70D ARG* 4.6 1.6 + - - -
74D ILE* 4.3 13.4 - - + +
75D ILE 4.5 0.9 - - - +
77D PRO* 4.2 27.4 - - + -
80D SER* 5.2 0.4 - - - +
81D PHE* 4.8 0.7 - - + -
104D ALA* 3.7 44.2 - - + +
107D ALA* 4.2 11.4 - - + -
108D VAL* 3.8 20.6 - - + -
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Residues in contact with LEU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D GLU* 3.0 41.9 + - + +
62D GLU* 4.4 2.5 - - - +
64D ILE* 1.3 78.0 - - - +
66D LEU* 1.3 71.6 + - + +
68D PHE 5.6 0.4 - - - +
70D ARG* 2.9 29.9 + - - +
74D ILE* 4.6 2.2 - - + -
76D TYR* 3.5 33.2 - - + -
77D PRO* 3.8 18.6 - - + -
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Residues in contact with LEU 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 3.7 30.5 - - + -
18D LYS* 4.0 28.0 - - + +
19D PHE* 5.6 0.2 - - - -
20D LEU* 3.7 32.8 - - + +
62D GLU* 2.9 17.5 + - + +
65D LEU* 1.3 87.9 - - + +
67D GLY* 1.3 61.9 + - - +
68D PHE 3.9 2.6 - - - +
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Residues in contact with GLY 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D TYR* 6.4 0.4 - - - -
20D LEU* 3.4 19.3 - - - +
63D ILE 2.7 18.4 + - - -
66D LEU* 1.3 75.3 - - - +
68D PHE* 1.3 63.2 + - - +
69D GLU* 3.4 2.4 + - - -
132D ASN* 4.7 0.5 - - - +
135D LYS* 4.7 9.5 + - - +
136D PHE* 3.7 22.8 - - - -
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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