Contacts of the helix formed by residues 45 - 56 (chain A) in PDB entry 1VYW
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 PRO 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A TYR* 5.8 4.5 - - + +
35A ILE* 4.2 19.7 - - + -
37A LEU* 3.7 13.7 - - + -
40A GLU* 3.9 18.8 - - + +
43A GLY 3.4 6.0 - - - +
44A VAL* 1.3 93.1 - - + +
46A SER* 1.3 64.0 + - - +
47A THR* 3.8 16.6 - - - +
48A ALA* 3.1 9.9 + - + +
49A ILE* 3.0 20.3 + - - +
76A LEU* 5.2 0.4 - - + -
266B LYS* 5.5 0.4 - - - -
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Residues in contact with SER 46 (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 VAL 3.6 1.6 + - - -
45A PRO* 1.3 71.6 - - - +
47A THR* 1.3 58.5 + - - +
49A ILE* 3.4 12.0 - - - +
50A ARG* 3.0 53.6 + - - +
266B LYS* 3.7 33.5 + - - +
272B PRO* 3.9 15.5 - - - +
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Residues in contact with THR 47 (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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15A TYR* 4.8 16.7 - - + +
35A ILE* 5.9 0.5 - - - +
45A PRO* 3.8 12.8 - - - +
46A SER* 1.3 76.0 - - - +
48A ALA* 1.3 61.7 + - - +
50A ARG* 3.4 3.4 + - - +
51A GLU* 2.8 32.3 + - - +
147A GLY* 3.6 33.8 - - - +
148A LEU* 4.7 11.9 - - + -
162A GLU* 4.9 8.3 - - - +
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Residues in contact with ALA 48 (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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35A ILE* 4.0 27.6 - - + -
44A VAL* 3.9 15.0 - - + -
45A PRO* 3.1 13.8 + - + +
47A THR* 1.3 77.3 + - - +
49A ILE* 1.3 68.8 + - - +
51A GLU* 4.6 5.2 - - - -
52A ILE* 2.8 37.7 + - + +
76A LEU* 4.0 9.4 - - + -
78A LEU* 5.3 3.1 - - + -
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Residues in contact with ILE 49 (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 VAL* 3.5 26.9 - - + +
45A PRO 3.0 18.0 + - - +
46A SER* 3.4 11.9 - - - +
48A ALA* 1.3 76.0 - - - +
50A ARG* 1.3 52.1 + - - +
52A ILE* 4.1 2.4 - - - +
53A SER* 2.7 39.2 + - - -
263B LEU* 3.9 24.0 - - + +
266B LYS* 4.4 11.0 - - + -
267B PHE* 4.2 28.9 - - + +
299B LEU* 4.0 14.4 - - + -
304B PHE* 4.7 6.5 - - + -
306B LEU* 3.6 21.9 - - + +
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Residues in contact with ARG 50 (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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46A SER* 3.0 34.2 + - - +
47A THR* 3.9 5.3 - - - +
49A ILE* 1.3 77.9 - - - +
51A GLU* 1.3 67.3 + - - +
53A SER* 3.7 4.7 - - - -
54A LEU* 2.9 34.5 + - + +
126A ARG* 5.6 0.7 - - - -
146A PHE 4.4 0.9 - - - +
147A GLY 4.2 10.7 + - - +
148A LEU* 5.4 1.2 - - - +
149A ALA 3.2 27.8 + - - +
150A ARG* 2.5 48.3 - - - +
162A GLU* 3.2 27.0 + - - -
266B LYS 3.3 19.2 + - - -
267B PHE* 3.3 30.1 + - + +
269B GLU 3.6 3.6 + - - -
270B ILE 4.7 2.6 + - - -
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Residues in contact with GLU 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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33A LYS* 2.7 33.6 + - - -
47A THR 2.8 20.9 + - - +
48A ALA* 4.1 4.3 - - - +
50A ARG* 1.3 72.2 - - - +
52A ILE* 1.3 59.1 + - - +
55A LEU* 2.8 56.8 + - + +
66A LEU* 6.0 0.2 - - + -
78A LEU* 3.9 8.5 - - + +
80A PHE* 3.9 15.1 - - + -
145A ASP* 3.6 10.0 + - - -
146A PHE* 2.9 47.5 + - + +
147A GLY* 4.1 5.7 + - - +
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Residues in contact with ILE 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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48A ALA 2.8 25.9 + - - +
49A ILE 4.1 0.2 - - - +
51A GLU* 1.3 72.9 - - - +
53A SER* 1.3 62.7 + - - +
56A LYS* 3.0 31.2 + - + +
66A LEU* 3.9 11.6 - - + +
69A VAL* 3.9 26.2 - - + -
76A LEU* 4.2 9.6 - - + -
78A LEU* 3.5 42.4 - - + -
304B PHE* 3.5 50.9 - - + -
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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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49A ILE 2.7 21.3 + - - -
50A ARG 3.4 2.8 + - - -
52A ILE* 1.3 80.0 - - - +
54A LEU* 1.3 63.8 + - - +
56A LYS* 3.7 13.6 - - - +
57A GLU* 4.0 16.8 + - - +
267B PHE* 3.3 24.8 - - - -
304B PHE* 3.2 26.0 - - - -
305B ASP* 5.5 1.7 - - - +
306B LEU* 3.9 20.2 - - - -
307B ALA 4.4 2.2 + - - -
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Residues in contact with LEU 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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50A ARG* 2.9 26.0 + - + +
51A GLU* 4.4 1.3 - - - +
53A SER* 1.3 79.1 - - - +
55A LEU* 1.3 66.3 + - - +
57A GLU* 3.1 14.5 + - - +
58A LEU* 3.2 21.1 + - + +
122A ARG* 4.5 3.6 - - - +
123A VAL* 4.0 27.9 - - + +
146A PHE* 5.3 2.2 - - + -
149A ALA* 3.8 19.1 - - + +
150A ARG* 3.8 35.0 - - - +
151A ALA* 4.0 13.5 - - + +
267B PHE* 4.3 6.1 - - + -
307B ALA* 4.0 25.1 - - + -
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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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51A GLU* 2.8 40.2 + - + +
52A ILE 4.0 0.9 - - - +
54A LEU* 1.3 73.7 - - - +
56A LYS* 1.3 57.0 + - - +
57A GLU 2.9 5.4 - - - -
58A LEU* 2.9 30.9 + - + +
63A ILE* 3.8 19.3 - - + -
64A VAL* 3.9 19.1 - - + +
66A LEU* 4.3 17.2 + - + +
80A PHE* 3.5 31.9 - - + -
146A PHE* 3.7 37.2 - - + -
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Residues in contact with LYS 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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52A ILE* 3.0 31.4 + - + +
53A SER 3.7 7.6 - - - +
55A LEU* 1.3 75.4 - - - +
57A GLU* 1.3 63.2 + - + +
58A LEU 3.4 1.1 - - - -
59A ASN* 5.8 1.7 - - - +
66A LEU* 4.4 16.5 - - + +
69A VAL* 5.4 4.9 - - - -
303B THR* 3.3 19.3 + - - -
304B PHE* 3.9 19.3 - - - +
305B ASP* 3.1 31.7 + - - +
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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