Contacts of the helix formed by residues 50 - 59 (chain A) in PDB entry 1VE3
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 GLY 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A CYS* 3.0 15.7 + - - -
48A GLY 3.2 2.8 + - - -
49A VAL* 1.3 78.1 - - - +
51A GLY* 1.3 65.9 + - - +
52A PHE 3.3 2.2 - - - -
53A SER* 3.0 18.6 + - - -
54A PHE* 3.1 21.0 + - - -
89A PHE* 3.8 24.5 - - - -
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Residues in contact with GLY 51 (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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16A ILE* 3.6 18.5 - - - +
21A TYR* 3.0 30.6 + - - -
25A ILE* 4.1 10.5 - - - +
47A CYS 4.5 0.6 + - - -
49A VAL 3.5 2.4 - - - -
50A GLY* 1.3 77.0 - - - +
52A PHE* 1.3 62.0 + - - +
54A PHE* 3.5 6.1 + - - +
55A LEU* 3.3 18.9 + - - +
83A ARG* 5.3 1.7 + - - -
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Residues in contact with PHE 52 (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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21A TYR* 4.5 2.2 + + - -
24A ARG* 3.8 27.1 - - + -
25A ILE* 3.7 41.7 - - + -
28A LEU* 3.9 25.8 - - + -
32A LEU* 4.1 13.0 - - + -
44A ASP* 4.1 12.5 + - - +
47A CYS 5.5 0.8 + - - -
50A GLY 3.3 0.4 - - - -
51A GLY* 1.3 75.1 - - - +
53A SER* 1.3 65.1 + - - +
55A LEU* 3.6 14.1 - - + +
56A LEU* 3.2 27.2 + - - +
108A ILE* 4.1 13.7 - - + -
110A ILE* 3.7 24.7 - - + -
302A SAM 3.7 30.7 - - - +
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Residues in contact with SER 53 (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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44A ASP* 2.8 33.3 + - - +
50A GLY* 3.0 11.7 + - - -
52A PHE* 1.3 76.1 - - - +
54A PHE* 1.3 61.0 + - - +
56A LEU* 3.0 6.7 + - - +
57A GLU* 2.8 30.2 + - - +
63A VAL* 3.7 23.9 - - - +
65A GLY* 4.4 0.3 - - - -
87A VAL* 3.9 15.4 - - - +
89A PHE* 3.9 15.2 - - - -
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Residues in contact with PHE 54 (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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16A ILE* 3.6 26.5 - - + -
49A VAL 3.8 1.3 - - - -
50A GLY 3.1 22.0 + - - -
51A GLY* 3.9 4.3 - - - +
53A SER* 1.3 75.7 - - - +
55A LEU* 1.3 62.6 + - - +
57A GLU* 3.3 7.3 + - - +
58A ASP* 3.0 34.2 + - - +
76A ALA 3.6 4.0 - - - -
79A TYR* 3.6 10.5 - - + -
80A ALA* 3.5 36.3 - - + -
83A ARG* 3.8 33.2 - - - +
85A SER* 3.4 28.9 - - - -
87A VAL* 4.3 2.5 - - + -
89A PHE* 3.6 25.8 - + - -
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Residues in contact with LEU 55 (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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25A ILE* 3.8 27.1 - - + -
29A GLU* 3.8 35.9 - - + +
32A LEU* 4.8 7.2 - - + -
33A MSE 5.5 0.9 - - + -
51A GLY 3.3 12.5 + - - +
52A PHE* 3.6 25.4 - - + +
53A SER 3.1 0.4 - - - -
54A PHE* 1.3 81.1 - - - +
56A LEU* 1.3 65.7 + - + +
58A ASP* 3.3 14.6 + - + +
59A TYR* 3.2 44.7 + - + -
83A ARG* 5.5 0.6 - - - +
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Residues in contact with LEU 56 (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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32A LEU* 4.9 8.1 - - + -
33A MSE 3.6 31.4 - - + -
36A MSE 3.5 24.0 - - + -
42A VAL* 3.5 35.0 - - + -
52A PHE 3.2 11.7 + - - +
53A SER 3.0 7.8 + - - +
55A LEU* 1.3 81.3 - - + +
57A GLU* 1.3 65.7 + - - +
59A TYR* 2.9 12.4 + - + -
61A PHE* 3.2 31.1 + - + -
63A VAL* 3.9 12.1 - - + -
108A ILE* 3.9 19.5 - - + -
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Residues in contact with GLU 57 (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 SER 2.8 16.1 + - - +
54A PHE* 3.6 7.7 - - - +
56A LEU* 1.3 76.4 - - - +
58A ASP* 1.3 71.7 + - - +
60A GLY* 3.3 12.6 + - - -
61A PHE 3.7 17.3 + - - +
63A VAL* 3.8 3.9 - - + +
84A GLU 5.1 0.2 - - - +
85A SER* 2.6 36.2 + - - -
86A ASN* 2.6 27.6 + - - +
87A VAL* 3.3 16.8 + - + +
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Residues in contact with ASP 58 (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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54A PHE* 3.0 25.2 + - - +
55A LEU* 3.7 10.5 - - + +
56A LEU 3.1 0.2 - - - -
57A GLU* 1.3 87.7 - - - +
59A TYR* 1.3 59.8 + - + +
60A GLY 3.1 5.8 + - - -
83A ARG* 5.1 5.0 + - - -
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Residues in contact with TYR 59 (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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29A GLU* 2.6 32.0 + - + +
33A MSE 3.9 35.1 - - + +
39A ARG* 3.1 39.7 + - - +
55A LEU* 3.2 46.8 + - + +
56A LEU* 2.9 11.4 + - - +
58A ASP* 1.3 79.5 - - + +
60A GLY* 1.3 58.4 + - - +
61A PHE* 4.0 11.2 - - + -
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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