Contacts of the helix formed by residues 66 - 78 (chain A) in PDB entry 5VEY
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 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ARG* 3.3 29.7 + - - +
64A THR* 4.2 12.6 - - + +
65A ILE* 1.3 80.4 - - - +
67A SER* 1.3 65.8 + - - +
68A ARG* 3.2 10.1 + - - +
69A GLU* 2.5 37.2 + - - +
70A ILE* 3.3 14.4 + - - +
133A GLY* 5.5 4.0 - - - -
136A ALA* 4.2 10.1 - - - +
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Residues in contact with SER 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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66A THR* 1.3 75.8 - - - +
68A ARG* 1.3 54.0 + - - +
70A ILE* 3.3 11.5 + - - +
71A GLN* 2.8 47.4 + - - +
94A VAL* 4.6 9.1 - - - +
135A GLY* 4.3 14.3 - - - -
136A ALA* 4.4 5.7 - - - +
139A TYR* 2.9 31.2 - - - -
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Residues in contact with ARG 68 (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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62A ARG* 4.4 15.5 - - - +
66A THR* 3.1 10.6 + - - +
67A SER* 1.3 79.6 - - - +
69A GLU* 1.3 69.6 + - - +
71A GLN* 3.4 16.6 + - - +
72A THR* 3.1 24.9 + - - -
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Residues in contact with GLU 69 (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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53A ALA* 4.4 9.6 - - + +
56A LEU* 3.1 44.5 - - + +
57A ALA* 4.2 15.0 - - + +
60A ASN* 3.5 25.5 + - - +
62A ARG* 3.1 28.6 + - - -
64A THR 4.3 3.0 - - - +
65A ILE* 4.0 10.7 - - + -
66A THR* 2.5 41.0 + - - +
68A ARG* 1.3 79.9 - - - +
70A ILE* 1.3 62.9 - - - +
72A THR* 3.4 3.1 + - - -
73A ALA* 3.3 6.4 + - - +
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Residues in contact with ILE 70 (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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49A ILE* 4.4 13.0 - - + -
53A ALA* 4.4 10.8 - - + -
65A ILE* 4.2 12.1 - - + -
66A THR 3.3 8.5 + - - +
67A SER* 3.3 7.9 + - - +
69A GLU* 1.3 74.7 - - - +
71A GLN* 1.3 55.2 + - - +
73A ALA* 3.1 7.4 + - - +
74A VAL* 2.8 55.4 + - + +
123A LEU* 5.7 4.5 - - + -
136A ALA* 3.1 51.6 - - + +
139A TYR* 3.7 18.2 - - + -
140A LEU* 4.6 12.1 - - + +
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Residues in contact with GLN 71 (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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67A SER* 2.8 43.4 + - - +
68A ARG* 3.5 16.5 - - - +
69A GLU 3.3 0.2 - - - -
70A ILE* 1.3 72.6 - - - +
72A THR* 1.3 62.7 + - - +
74A VAL* 3.4 3.1 + - - +
75A ARG* 3.2 37.0 + - - +
87A VAL* 5.7 7.6 - - + +
91A THR* 4.2 12.7 + - - +
139A TYR* 3.3 40.2 + - + +
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Residues in contact with THR 72 (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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56A LEU* 3.9 18.8 - - + -
68A ARG 3.1 14.0 + - - -
69A GLU* 3.7 7.6 - - - -
70A ILE 3.2 0.4 - - - -
71A GLN* 1.3 77.9 - - - +
73A ALA* 1.3 63.5 + - - +
75A ARG* 3.4 26.4 + - - +
76A LEU* 3.2 41.5 + - + +
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Residues in contact with ALA 73 (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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49A ILE* 4.5 10.8 - - + +
52A GLU* 3.0 53.8 - - + +
53A ALA 4.3 5.6 - - - +
56A LEU* 3.9 6.0 - - + +
69A GLU 3.3 9.6 + - - +
70A ILE* 3.1 11.3 + - - +
72A THR* 1.3 76.7 - - - +
74A VAL* 1.3 66.4 + - - +
76A LEU 3.3 0.9 + - - -
77A LEU* 3.1 18.8 + - - +
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Residues in contact with VAL 74 (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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49A ILE* 4.8 13.9 - - + -
70A ILE* 2.8 46.9 + - + +
71A GLN* 3.6 6.7 - - - +
72A THR 3.3 0.2 - - - -
73A ALA* 1.3 74.9 - - - +
75A ARG* 1.3 60.4 + - + +
77A LEU* 3.3 4.7 + - - -
78A LEU* 2.8 37.8 + - + +
83A ALA 5.3 0.2 - - - +
86A ALA* 3.6 30.7 - - + -
87A VAL* 6.2 0.7 - - + -
139A TYR* 3.9 15.0 - - + +
140A LEU* 5.4 0.2 - - + -
143A VAL* 4.3 21.5 - - + -
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Residues in contact with ARG 75 (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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71A GLN* 3.2 20.4 + - - +
72A THR* 3.8 35.0 + - - +
73A ALA 3.3 0.2 - - - -
74A VAL* 1.3 78.5 - - + +
76A LEU* 1.3 59.4 + - + +
78A LEU 2.8 21.8 - - - +
83A ALA* 4.0 23.7 - - + +
87A VAL* 4.6 21.3 - - + -
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Residues in contact with LEU 76 (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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52A GLU* 3.1 29.4 - - + +
56A LEU* 5.4 5.6 - - + -
72A THR* 3.2 32.2 + - + +
73A ALA* 3.7 1.3 - - - +
74A VAL 3.3 0.2 - - - -
75A ARG* 1.3 79.4 - - + +
77A LEU* 1.3 61.3 + - + +
78A LEU 4.7 0.7 - - - +
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Residues in contact with LEU 77 (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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48A ARG* 3.5 42.8 + - + +
49A ILE* 3.6 39.5 - - + +
52A GLU* 2.8 29.6 - - + +
73A ALA 3.1 8.7 + - - +
74A VAL* 4.0 3.1 - - - +
76A LEU* 1.3 82.0 - - - +
78A LEU* 1.3 64.7 + - + +
79A PRO* 4.0 2.8 - - - +
185A LEU* 3.1 31.5 - - + +
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Residues in contact with LEU 78 (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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45A ILE* 6.1 1.1 - - + -
49A ILE* 5.9 4.7 - - + -
74A VAL* 2.8 24.9 + - + +
75A ARG 2.8 21.5 - - - +
76A LEU 4.6 0.9 - - - +
77A LEU* 1.3 83.0 - - + +
79A PRO* 1.3 71.5 - - + +
82A LEU* 3.7 35.4 - - + +
83A ALA* 3.7 12.8 - - - +
86A ALA* 3.9 15.9 - - + -
143A VAL* 4.7 8.7 - - + -
146A TYR* 5.2 4.9 - - + -
147A LEU* 4.5 24.7 - - + -
185A LEU* 3.9 23.3 - - + -
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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