Contacts of the helix formed by residues 41 - 58 (chain P) in PDB entry 2L7F
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 THR 41 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4P GLN 5.8 3.8 - - - +
6P THR* 5.2 2.5 - - - +
35P ALA* 3.7 2.0 - - - -
40P LEU* 1.3 78.2 - - - +
42P GLU* 1.3 59.0 + - - +
43P ALA* 3.6 8.8 + - - +
44P ARG* 3.1 46.3 + - - +
45P VAL* 3.0 28.8 + - - +
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Residues in contact with GLU 42 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P MET* 5.0 6.0 - - - +
31P ARG* 4.8 3.9 - - + +
32P GLU* 4.0 45.5 - - + +
35P ALA* 3.8 10.8 - - - +
41P THR* 1.3 72.9 - - - +
43P ALA* 1.3 69.5 + - - +
45P VAL* 3.7 4.9 + - - +
46P ARG* 2.8 72.3 + - - +
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Residues in contact with ALA 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41P THR* 3.2 9.1 + - - +
42P GLU* 1.3 89.3 + - - +
44P ARG* 1.3 59.9 + - + +
46P ARG* 3.2 11.1 + - - +
47P VAL* 3.0 34.4 + - + +
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Residues in contact with ARG 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4P GLN 4.5 4.4 + - - -
5P ARG* 3.8 26.4 - - - +
6P THR* 2.8 60.9 + - - +
8P PHE* 3.4 27.5 - - + -
40P LEU* 4.8 5.2 - - + -
41P THR* 3.1 36.8 + - - +
43P ALA* 1.3 74.5 - - + +
45P VAL* 1.3 56.5 + - - +
47P VAL* 3.5 7.9 + - - +
48P TRP 3.0 22.5 + - - -
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Residues in contact with VAL 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8P PHE* 5.1 0.2 - - - -
16P LEU* 4.4 6.5 - - + -
31P ARG* 3.8 16.8 - - + +
34P ILE* 3.6 27.1 - - + -
35P ALA* 3.7 22.9 - - + -
38P THR* 4.5 0.2 - - - +
40P LEU* 4.0 20.6 - - + -
41P THR 3.0 18.0 + - - +
42P GLU* 3.8 6.3 - - - +
44P ARG* 1.3 72.2 - - - +
46P ARG* 1.3 58.3 + - - +
48P TRP* 3.1 9.9 + - - +
49P PHE* 2.9 44.3 + - + -
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Residues in contact with ARG 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P MET* 4.2 29.5 + - - +
31P ARG* 4.7 22.8 - - - +
42P GLU* 2.8 65.9 + - - +
43P ALA* 3.2 12.7 + - - +
45P VAL* 1.3 74.6 - - - +
47P VAL* 1.3 57.5 + - + +
49P PHE* 3.4 9.3 + - - +
50P LYS* 3.0 29.0 + - + +
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Residues in contact with VAL 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8P PHE* 5.0 8.7 - - + -
43P ALA 3.0 18.8 + - - +
44P ARG* 3.6 11.2 - - - +
45P VAL 3.3 0.2 - - - -
46P ARG* 1.3 75.1 - - + +
48P TRP* 1.3 56.1 + - - +
50P LYS* 3.4 11.1 + - + +
51P ASN* 2.9 33.8 + - + +
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Residues in contact with TRP 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8P PHE* 3.8 26.2 - + + -
13P LEU* 3.5 31.8 - - + +
16P LEU* 3.3 67.6 - - + +
17P GLU* 3.8 10.3 - - + -
20P PHE* 3.9 16.6 - + + -
44P ARG 3.0 15.0 + - - +
45P VAL* 3.1 11.8 + - - +
47P VAL* 1.3 74.0 - - - +
49P PHE* 1.3 71.3 + + - +
51P ASN* 3.3 8.8 + - + +
52P ARG* 2.8 70.0 + - + +
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Residues in contact with PHE 49 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P LEU* 4.6 4.7 - - + -
19P THR* 4.0 17.0 - - + -
20P PHE* 4.0 20.0 - + - -
23P ASN 3.9 7.4 - - - -
24P ARG 3.5 21.5 - - - -
26P PRO* 3.5 31.9 - - + -
31P ARG* 3.8 37.9 - - + +
34P ILE* 4.5 6.3 - - + -
45P VAL* 2.9 44.5 + - + -
46P ARG 3.8 6.3 - - - +
48P TRP* 1.3 86.5 - + - +
50P LYS* 1.3 56.6 + - - +
52P ARG* 3.4 2.6 + - - +
53P ARG* 2.9 31.2 + - - +
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Residues in contact with LYS 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46P ARG* 3.0 17.9 + - + +
47P VAL* 3.6 11.9 - - + +
49P PHE* 1.3 74.7 - - - +
51P ASN* 1.3 56.7 + - - +
53P ARG* 3.5 7.2 + - - +
54P ALA* 3.0 29.8 + - + +
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Residues in contact with ASN 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8P PHE* 6.3 2.2 - - + -
47P VAL* 2.9 25.0 + - + +
48P TRP* 3.6 10.4 - - + +
50P LYS* 1.3 73.0 - - - +
52P ARG* 1.3 56.2 + - - +
54P ALA* 3.3 7.6 + - - +
55P LYS* 2.9 59.5 + - - +
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Residues in contact with ARG 52 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17P GLU* 2.8 34.5 + - - +
20P PHE* 3.5 41.9 - - + -
21P GLN* 6.1 0.4 - - - +
48P TRP* 2.8 51.9 + - + +
49P PHE* 3.7 5.2 - - - +
51P ASN* 1.3 71.6 + - - +
53P ARG* 1.3 56.8 - - - +
55P LYS* 3.5 7.1 + - - +
56P TRP* 3.0 45.2 + - - +
64P VAL* 4.9 25.9 - - - +
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Residues in contact with ARG 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P PHE* 5.1 7.7 - - + -
49P PHE 2.9 18.1 + - - +
50P LYS* 3.7 6.1 - - - +
52P ARG* 1.3 73.0 - - - +
54P ALA* 1.3 58.5 + - - +
56P TRP* 3.3 28.3 + - + +
57P ARG* 2.9 36.6 + - + +
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Residues in contact with ALA 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50P LYS* 3.0 19.0 + - + +
51P ASN* 3.5 9.2 - - - +
53P ARG* 1.3 74.9 - - - +
55P LYS* 1.3 55.7 + - + +
57P ARG* 3.2 6.5 + - - +
58P LYS* 2.9 40.1 + - + +
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Residues in contact with LYS 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51P ASN* 2.9 44.7 + - - +
52P ARG* 3.7 11.9 - - - +
54P ALA* 1.3 72.6 - - + +
56P TRP* 1.3 61.3 + - - +
58P LYS* 3.9 22.7 + - + +
63P ILE* 2.9 63.2 + - + +
64P VAL* 4.0 16.9 - - + +
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Residues in contact with TRP 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P PHE* 5.3 7.4 - + + -
24P ARG* 4.4 20.8 - - - +
52P ARG* 3.0 33.5 + - - +
53P ARG* 3.5 32.8 - - + +
55P LYS* 1.3 78.1 - - - +
57P ARG* 1.3 84.9 + - + +
58P LYS 4.2 3.5 - - - +
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Residues in contact with ARG 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53P ARG* 2.9 23.0 + - - +
54P ALA* 3.2 6.9 + - - +
56P TRP* 1.3 96.7 - - + +
58P LYS* 1.3 63.1 + - - +
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Residues in contact with LYS 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54P ALA* 2.9 23.2 + - + +
55P LYS* 3.9 28.4 - - + +
56P TRP 4.2 5.0 - - - +
57P ARG* 1.3 81.1 - - - +
59P ARG* 1.3 65.5 + - - +
60P GLU* 3.4 32.7 + - + +
63P ILE* 4.9 8.1 - - + +
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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