Contacts of the helix formed by residues 44 - 58 (chain A) in PDB entry 2FVY
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 ASP 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A SER 3.1 7.1 + - - +
42A GLN 4.0 3.6 - - - +
43A ASN* 1.3 77.9 - - - +
45A GLN* 1.3 65.0 + - - +
46A SER* 2.9 25.4 + - - -
47A LYS* 3.1 39.6 + - + +
48A GLN* 3.1 19.2 + - - +
68A VAL* 3.6 5.0 - - - +
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Residues in contact with GLN 45 (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* 1.3 74.6 + - - +
46A SER* 1.3 57.3 + - - +
48A GLN* 3.0 24.4 + - - +
49A ASN* 2.8 55.8 + - - +
67A LEU* 3.9 5.3 - - - +
68A VAL* 2.9 27.5 + - + +
69A ASP* 2.9 37.9 + - + +
72A ALA* 3.5 29.2 - - + +
76A VAL* 4.3 2.6 - - - +
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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 ASP* 2.9 13.2 + - - -
45A GLN* 1.3 77.6 - - - +
47A LYS* 1.3 62.9 + - - +
49A ASN* 3.3 11.4 + - - +
50A ASP* 3.2 28.8 + - - +
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Residues in contact with LYS 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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40A ASP 5.9 0.2 - - - +
41A SER* 3.7 14.1 - - - +
42A GLN* 2.8 37.1 + - + +
44A ASP* 3.1 36.5 + - + +
46A SER* 1.3 77.7 - - - +
48A GLN* 1.3 57.6 + - - +
50A ASP* 3.3 8.5 + - - +
51A GLN* 2.9 37.9 + - - +
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Residues in contact with GLN 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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8A THR* 3.2 25.6 + - - +
10A TYR* 4.2 1.4 - - - +
41A SER* 3.0 31.9 + - - +
44A ASP 3.1 8.7 + - - +
45A GLN* 3.0 31.3 + - - +
47A LYS* 1.3 77.7 - - - +
49A ASN* 1.3 62.4 + - - +
51A GLN* 3.1 11.9 + - - +
52A ILE* 2.9 29.4 + - + +
65A ILE* 3.7 3.8 - - - +
66A ASN 2.9 23.2 + - - -
67A LEU* 3.3 23.0 - - - +
68A VAL* 3.9 8.2 - - + +
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Residues in contact with ASN 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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45A GLN* 2.8 53.1 + - - +
46A SER* 3.7 9.9 + - - +
47A LYS 3.3 0.2 - - - -
48A GLN* 1.3 72.6 - - - +
50A ASP* 1.3 65.7 + - - +
52A ILE* 3.2 5.7 + - - +
53A ASP* 3.1 25.5 + - - -
72A ALA* 4.8 1.5 - - - +
75A THR* 4.0 27.7 - - - +
76A VAL* 4.2 8.5 - - - +
79A LYS* 3.6 19.0 - - - +
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Residues in contact with ASP 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 3.2 14.3 + - - +
47A LYS* 3.7 8.4 - - - +
49A ASN* 1.3 76.6 - - - +
51A GLN* 1.3 67.2 + - + +
53A ASP* 3.2 16.2 + - - +
54A VAL* 3.1 27.4 + - + +
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Residues in contact with GLN 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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8A THR* 4.4 5.6 - - + +
39A ASN* 3.6 40.1 - - + +
40A ASP 2.9 24.5 + - - +
41A SER* 2.8 32.1 + - - +
47A LYS* 2.9 20.3 + - + +
48A GLN* 3.1 9.9 + - - +
50A ASP* 1.3 77.3 - - + +
52A ILE* 1.3 57.3 + - - +
54A VAL* 3.2 9.6 + - - +
55A LEU* 2.9 32.5 + - - +
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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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8A THR* 4.1 8.7 - - + -
48A GLN* 2.9 31.8 + - + +
49A ASN* 3.6 9.0 - - - +
50A ASP 3.2 0.4 - - - -
51A GLN* 1.3 72.3 - - - +
53A ASP* 1.3 67.1 + - - +
55A LEU* 3.2 7.4 + - + +
56A LEU* 2.9 36.8 + - + +
63A LEU* 4.1 17.0 - - + -
65A ILE* 3.9 28.3 - - + -
76A VAL* 3.6 34.8 - - + +
79A LYS* 3.9 20.0 - - + -
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Residues in contact with ASP 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 ASN 3.1 12.0 + - - +
50A ASP* 3.2 18.7 + - - +
52A ILE* 1.3 77.1 - - - +
54A VAL* 1.3 57.5 + - + +
56A LEU* 3.4 7.4 + - - +
57A ALA* 2.9 28.5 + - - +
79A LYS* 2.8 41.0 + - - +
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Residues in contact with VAL 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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39A ASN* 6.1 0.4 - - - +
50A ASP* 3.1 15.6 + - + +
51A GLN* 3.5 9.6 - - - +
53A ASP* 1.3 78.4 - - + +
55A LEU* 1.3 65.8 + - + +
57A ALA* 3.1 8.4 + - + +
58A LYS* 3.0 53.7 + - + +
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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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6A GLY* 3.9 15.9 - - - -
7A VAL 4.1 1.1 - - - +
8A THR* 3.9 21.8 - - + -
37A LEU* 3.6 41.7 - - + +
39A ASN* 3.9 19.1 - - - +
51A GLN 2.9 19.8 + - - +
52A ILE* 3.2 7.2 + - + +
54A VAL* 1.3 77.8 - - + +
56A LEU* 1.3 62.1 + - - +
58A LYS* 3.2 16.5 + - + +
59A GLY 3.3 7.6 + - - -
60A VAL* 3.3 19.2 + - + +
63A LEU* 3.8 28.7 - - + -
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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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52A ILE* 2.9 26.7 + - + +
53A ASP* 3.7 7.0 - - - +
55A LEU* 1.3 72.1 - - - +
57A ALA* 1.3 65.5 + - - +
59A GLY* 3.0 9.2 + - - +
60A VAL* 4.3 6.3 - - + -
63A LEU* 4.1 15.3 - - + -
79A LYS* 3.5 42.4 - - + +
80A ALA* 4.1 2.7 - - - +
83A GLN* 2.9 43.9 + - + +
85A VAL* 3.8 36.6 - - + -
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Residues in contact with ALA 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 ASP 2.9 14.8 + - - +
54A VAL* 3.1 13.4 + - + +
56A LEU* 1.3 75.6 - - - +
58A LYS* 1.3 58.9 + - + +
59A GLY* 3.3 3.8 + - - -
83A GLN* 5.2 0.9 - - - -
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Residues in contact with LYS 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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4A ARG* 3.0 36.7 + - - +
37A LEU* 4.1 30.0 - - + +
54A VAL* 3.0 38.9 + - + +
55A LEU* 3.5 12.9 - - + +
56A LEU 3.1 0.2 - - - -
57A ALA* 1.3 76.8 - - + +
59A GLY* 1.3 61.4 + - - +
60A VAL 3.4 0.9 - - - -
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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