Contacts of the helix formed by residues 2 - 18 (chain A) in PDB entry 2FVA
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 LYS 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A ALA 1.3 69.8 - - - -
3A LYS* 1.3 59.2 - - - +
4A GLU* 3.8 31.0 - - + +
5A THR* 3.3 4.0 + - - +
6A ILE* 2.9 29.9 + - - +
75A GLU* 2.3 35.0 + - + +
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Residues in contact with LYS 3 (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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1A ALA 5.3 1.3 - - - +
2A LYS* 1.3 73.7 - - - +
4A GLU* 1.3 54.8 + - - +
6A ILE* 3.6 12.5 - - + +
7A ASP* 2.8 49.3 + - - +
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Residues in contact with GLU 4 (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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2A LYS* 3.8 21.0 - - + +
3A LYS* 1.3 80.1 - - - +
5A THR* 1.3 83.3 + - - +
7A ASP* 3.5 6.7 + - - +
8A LYS* 3.1 28.0 + - - +
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Residues in contact with THR 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS* 3.3 14.3 + - - +
4A GLU* 1.3 88.3 + - - +
6A ILE* 1.3 61.3 + - - +
8A LYS* 3.1 7.8 + - - +
9A VAL* 2.9 34.5 + - + +
52A PHE* 3.7 25.3 - - + -
71A ALA* 3.9 25.4 - - - +
74A ILE* 4.1 11.0 - - + -
75A GLU* 3.9 16.0 + - + +
78A LEU* 4.7 5.7 - - + +
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Residues in contact with ILE 6 (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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1A ALA* 3.6 18.2 - - + +
2A LYS 2.9 22.6 + - - +
3A LYS* 3.6 11.7 - - + +
5A THR* 1.3 76.8 - - - +
7A ASP* 1.3 66.8 + - - +
9A VAL* 3.3 4.0 + - - +
10A SER* 3.0 25.6 + - - -
26A THR 5.4 0.7 - - - -
27A ALA* 3.5 27.6 - - + +
67A ILE* 4.0 7.9 - - + +
68A GLN* 3.1 27.8 - - - +
71A ALA* 3.4 24.9 - - + -
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Residues in contact with ASP 7 (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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3A LYS* 2.8 33.3 + - - +
4A GLU* 3.8 6.8 - - - +
6A ILE* 1.3 78.6 - - - +
8A LYS* 1.3 58.4 + - + +
10A SER* 2.9 15.7 + - - -
11A ASP* 2.8 33.5 + - - +
25A VAL* 5.1 9.7 - - - +
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Residues in contact with LYS 8 (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 GLU* 3.1 17.6 + - + +
5A THR 3.1 7.8 + - - +
7A ASP* 1.3 76.1 - - + +
9A VAL* 1.3 59.9 + - - +
11A ASP* 3.1 16.9 + - + +
12A ILE* 2.7 29.7 + - - +
51A GLU* 3.0 38.6 - - - +
52A PHE* 3.6 29.3 - - + -
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Residues in contact with VAL 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A THR 2.9 21.7 + - - +
6A ILE 3.7 4.0 - - - +
8A LYS* 1.3 74.8 - - - +
10A SER* 1.3 62.4 + - - +
12A ILE* 3.2 18.9 + - - +
13A VAL* 3.7 7.6 + - - +
31A PHE* 3.6 31.1 - - + -
48A LEU* 3.8 19.1 - - + -
52A PHE* 4.1 4.0 - - + -
67A ILE* 3.8 13.2 - - + -
70A ALA* 3.9 8.1 - - + -
71A ALA* 4.1 13.2 - - - -
74A ILE* 3.4 30.1 - - + -
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Residues in contact with SER 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 3.0 15.4 + - - -
7A ASP* 2.9 21.8 + - - -
9A VAL* 1.3 77.9 - - - +
11A ASP* 1.3 62.8 + - - +
13A VAL* 3.3 14.7 + - - +
14A LYS* 3.3 18.2 + - - +
25A VAL* 3.1 32.1 - - - +
26A THR 4.6 1.6 - - - -
67A ILE* 3.8 26.4 - - - +
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Residues in contact with ASP 11 (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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7A ASP* 2.8 31.2 + - - +
8A LYS* 3.2 14.7 - - + +
10A SER* 1.3 79.6 + - - +
12A ILE* 1.3 67.4 + - + +
14A LYS* 3.2 15.9 + - - +
15A GLU* 3.0 37.4 + - + +
25A VAL* 5.3 2.6 - - - +
51A GLU* 5.6 1.8 - - - +
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Residues in contact with ILE 12 (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 LYS 2.7 32.9 + - - +
9A VAL 3.2 9.3 + - - +
11A ASP* 1.3 77.7 - - + +
13A VAL* 1.3 64.2 + - + +
15A GLU* 3.2 18.1 + - - +
16A LYS* 3.2 13.3 + - + +
44A ILE* 3.8 29.6 - - + +
47A ASN* 3.3 45.4 - - + +
48A LEU* 3.7 19.3 - - + -
51A GLU* 3.2 33.9 - - + +
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Residues in contact with VAL 13 (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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9A VAL 3.9 8.3 - - - +
10A SER* 3.3 9.8 + - - +
11A ASP 3.2 0.6 - - - -
12A ILE* 1.3 78.3 - - + +
14A LYS* 1.3 60.3 + - + +
16A LYS* 2.8 35.1 - - + +
17A LEU* 3.3 9.8 - - + +
31A PHE* 3.5 51.1 - - + +
33A LYS* 6.3 4.0 - - + -
44A ILE* 4.2 12.3 - - + -
67A ILE* 5.2 3.8 - - + -
102A STE 5.6 8.3 - - + -
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Residues in contact with LYS 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER 3.3 16.1 + - - +
11A ASP* 3.2 15.6 + - - +
13A VAL* 1.3 72.8 - - + +
15A GLU* 1.3 54.3 + - + +
16A LYS 2.9 5.4 + - - -
17A LEU* 3.0 6.8 + - - +
18A ALA 2.7 31.5 + - - -
19A LEU* 2.9 37.0 + - + +
20A GLY* 3.4 33.2 - - - +
23A VAL* 4.1 18.7 - - - +
24A VAL 3.8 5.7 + - - -
25A VAL* 3.3 41.2 - - + +
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Residues in contact with GLU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 3.0 29.9 + - + +
12A ILE* 3.4 10.7 - - - +
13A VAL 3.2 0.4 - - - -
14A LYS* 1.3 76.0 - - + +
16A LYS* 1.3 62.8 + - - +
17A LEU 3.4 0.2 + - - -
18A ALA* 3.6 9.8 + - - +
47A ASN* 3.6 22.7 + - - +
51A GLU* 4.5 11.7 - - - +
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Residues in contact with LYS 16 (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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12A ILE* 3.2 14.8 - - + +
13A VAL* 2.8 30.7 - - + +
15A GLU* 1.3 81.2 - - - +
17A LEU* 1.3 58.4 + - + +
40A ASP* 3.7 20.2 - - - +
43A GLU* 3.0 45.9 + - - +
44A ILE* 3.7 28.6 - - + +
47A ASN* 5.0 5.4 - - + +
101A PNS 3.4 40.2 - - - +
102A STE 6.4 0.2 - - - -
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Residues in contact with LEU 17 (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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13A VAL* 3.3 24.9 - - + +
14A LYS* 3.8 5.4 - - - +
16A LYS* 1.3 78.4 - - + +
18A ALA* 1.3 75.8 + - - +
19A LEU* 3.6 36.9 - - + +
33A LYS* 5.8 8.7 - - + +
101A PNS 4.6 24.9 - - + +
102A STE 6.4 0.4 - - + -
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Residues in contact with ALA 18 (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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14A LYS 2.7 12.2 + - - -
15A GLU* 3.6 9.2 + - - +
16A LYS 3.6 2.4 - - - -
17A LEU* 1.3 81.9 - - - +
19A LEU* 1.3 65.4 + - - +
21A ALA* 6.0 0.7 - - - +
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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