Contacts of the helix formed by residues 49 - 67 (chain A) in PDB entry 1YVP
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 GLU 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A GLY 5.8 0.2 - - - -
44A GLY* 4.1 0.4 - - - -
47A TYR 4.2 1.3 + - - +
48A ILE* 1.3 78.2 - - - +
50A GLU* 1.3 66.8 + - - +
51A LYS* 3.3 4.5 - - + +
52A LYS* 3.0 15.7 + - + +
53A LEU* 2.8 20.6 + - - +
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Residues in contact with GLU 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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41A SER* 3.9 9.3 + - - +
42A GLU* 3.5 15.4 - - - +
43A GLY* 2.6 32.3 + - - +
44A GLY* 3.7 22.8 - - - +
49A GLU* 1.3 70.9 - - - +
51A LYS* 1.3 67.1 + - - +
53A LEU* 3.1 4.3 + - - +
54A GLY* 2.9 19.2 + - - -
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Residues in contact with LYS 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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49A GLU* 3.3 3.2 - - + +
50A GLU* 1.3 80.9 - - - +
52A LYS* 1.3 64.3 + - - +
54A GLY* 3.1 4.2 + - - +
55A GLN* 3.0 52.7 + - + +
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Residues in contact with LYS 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 ILE* 3.6 19.9 - - + +
49A GLU* 3.0 17.9 + - + +
51A LYS* 1.3 78.8 - - - +
53A LEU* 1.3 62.6 + - - +
55A GLN* 3.2 16.5 + - - +
56A GLU* 2.9 41.0 + - + +
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Residues in contact with LEU 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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32A ARG* 3.6 9.9 - - - +
40A GLY 4.4 0.4 - - - +
41A SER* 3.7 18.2 - - - +
44A GLY* 3.6 28.9 - - - -
45A THR* 3.9 11.2 - - + -
48A ILE* 3.6 19.0 - - + +
49A GLU 2.8 16.1 + - - +
50A GLU 3.5 8.5 - - - +
52A LYS* 1.3 72.9 - - - +
54A GLY* 1.3 62.3 + - - +
56A GLU* 3.3 5.6 + - - +
57A ASN* 3.2 33.7 + - - +
503A SER* 3.4 43.1 - - - +
504A ASN* 4.2 5.2 - - - -
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Residues in contact with GLY 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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36A PHE* 5.3 3.2 - - - -
41A SER* 3.5 20.6 - - - -
50A GLU 2.9 13.1 + - - -
51A LYS* 3.1 4.2 + - - -
53A LEU* 1.3 77.8 - - - +
55A GLN* 1.3 56.2 + - - +
57A ASN* 3.4 3.0 + - - +
58A ALA* 2.9 29.4 + - - +
94A PHE* 5.4 2.6 - - - -
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Residues in contact with GLN 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 LYS* 3.0 39.7 + - + +
52A LYS* 3.6 20.5 + - - +
54A GLY* 1.3 72.3 - - - +
56A GLU* 1.3 56.2 + - - +
58A ALA* 3.2 8.0 + - - +
59A GLU* 2.7 45.7 + - + +
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Residues in contact with GLU 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 ARG* 2.6 45.0 + - - +
48A ILE* 3.8 27.5 - - - +
52A LYS* 2.9 36.5 + - + +
53A LEU* 3.5 6.9 - - - +
54A GLY 3.3 0.2 - - - -
55A GLN* 1.3 77.3 - - - +
57A ASN* 1.3 61.1 + - - +
59A GLU* 3.2 18.1 + - - +
60A ALA* 3.1 20.8 + - - +
63A ARG* 5.1 1.0 + - - -
505A GLY 4.4 3.1 + - - -
506A PHE* 5.7 3.8 - - - -
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Residues in contact with ASN 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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32A ARG* 3.1 38.2 + - - +
33A LEU* 5.4 0.4 - - - +
36A PHE* 3.5 48.5 - - + +
41A SER* 4.7 0.3 - - - -
53A LEU* 3.2 22.4 + - - +
54A GLY 4.0 3.4 - - - +
56A GLU* 1.3 76.2 - - - +
58A ALA* 1.3 65.2 + - - +
60A ALA* 3.2 7.5 + - - +
61A LEU* 3.0 23.6 + - - +
503A SER* 3.0 28.3 + - - +
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Residues in contact with ALA 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 GLY 2.9 18.6 + - - +
55A GLN* 3.5 9.6 - - - +
57A ASN* 1.3 75.3 - - - +
59A GLU* 1.3 64.4 + - - +
61A LEU* 3.2 9.5 + - - +
62A LEU* 3.0 31.2 + - + +
94A PHE* 4.5 26.2 - - + -
98A VAL* 5.7 2.2 - - + +
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Residues in contact with GLU 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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55A GLN* 2.7 25.1 + - + +
56A GLU* 3.2 22.0 - - - +
58A ALA* 1.3 77.3 - - - +
60A ALA* 1.3 57.6 + - - +
62A LEU* 3.2 10.7 + - + +
63A ARG* 2.9 46.8 + - - +
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Residues in contact with ALA 60 (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 ASP* 3.5 22.6 - - + +
32A ARG* 4.2 24.0 - - + +
33A LEU* 5.9 0.9 - - - +
56A GLU 3.1 8.9 + - - +
57A ASN* 3.5 9.2 - - - +
59A GLU* 1.3 79.8 - - - +
61A LEU* 1.3 58.4 + - - +
63A ARG* 3.3 19.0 + - - +
64A LEU* 3.0 33.9 + - - +
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Residues in contact with LEU 61 (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 LEU* 4.6 14.1 - - + -
36A PHE* 5.8 2.9 - - + -
57A ASN 3.0 14.3 + - - +
58A ALA* 3.4 10.1 - - - +
59A GLU 3.2 0.2 - - - -
60A ALA* 1.3 74.4 - - - +
62A LEU* 1.3 66.5 + - - +
64A LEU* 3.0 11.4 + - + +
65A ILE* 3.0 28.3 + - + +
73A VAL* 3.9 31.6 - - + -
94A PHE* 4.8 8.5 - - + -
95A ALA* 3.7 24.2 - - + -
98A VAL* 3.7 32.3 - - + -
99A CYS* 4.3 9.9 - - - -
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Residues in contact with LEU 62 (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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58A ALA* 3.0 18.0 + - + +
59A GLU* 3.6 11.4 - - + +
61A LEU* 1.3 76.8 - - - +
63A ARG* 1.3 56.7 + - - +
65A ILE* 3.4 10.0 + - + +
66A GLU* 2.8 30.3 + - - +
98A VAL* 3.7 28.7 - - + -
139A MET* 4.5 17.9 - - + -
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Residues in contact with ARG 63 (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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26A GLN* 5.9 6.1 - - - +
29A ASP* 2.6 45.0 + - - +
56A GLU 5.1 0.6 + - - -
59A GLU* 2.9 42.0 + - - +
60A ALA* 3.4 18.5 - - - +
61A LEU 3.1 0.2 - - - -
62A LEU* 1.3 75.4 - - - +
64A LEU* 1.3 60.4 + - - +
66A GLU* 3.7 5.3 - - + +
67A ASP* 2.9 49.4 + - - +
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Residues in contact with LEU 64 (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 ASP* 3.5 39.5 - - + +
30A MET* 4.0 29.6 - - + -
33A LEU* 4.3 11.4 - - + -
60A ALA 3.0 18.1 + - - +
61A LEU* 3.0 14.8 + - + +
63A ARG* 1.3 76.7 - - - +
65A ILE* 1.3 60.5 + - - +
67A ASP* 3.3 10.7 + - - +
69A LYS* 2.9 47.5 + - + +
70A GLY 4.4 0.7 - - - -
73A VAL* 3.7 26.0 - - + -
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Residues in contact with ILE 65 (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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61A LEU* 3.0 19.1 + - + +
62A LEU* 3.7 12.1 - - + +
64A LEU* 1.3 76.6 - - + +
66A GLU* 1.3 58.1 + - - +
68A GLY* 2.9 20.3 + - - -
70A GLY* 4.1 18.4 - - - +
73A VAL* 5.1 0.7 - - + -
98A VAL* 4.1 23.8 - - + -
99A CYS* 4.1 17.3 - - - -
103A SER* 3.0 48.2 - - - +
104A ASP* 3.8 19.4 - - - +
107A THR* 4.4 2.2 - - + +
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Residues in contact with GLU 66 (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 LEU 2.8 18.7 + - - +
63A ARG* 3.7 8.3 - - - +
64A LEU 3.3 0.2 - - - -
65A ILE* 1.3 77.6 - - - +
67A ASP* 1.3 64.4 + - - +
68A GLY 3.0 4.2 + - - -
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Residues in contact with ASP 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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29A ASP* 4.8 3.3 - - - +
63A ARG* 2.9 40.0 + - - +
64A LEU* 3.7 7.0 - - - +
65A ILE 3.2 0.2 - - - -
66A GLU* 1.3 82.5 - - - +
68A GLY* 1.3 61.6 + - - +
69A LYS* 3.4 18.4 + - + +
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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