Contacts of the helix formed by residues 11 - 20 (chain P) in PDB entry 5L4K
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 GLY 11 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7P GLU 3.4 5.5 + - - -
8P ARG* 3.9 9.8 + - - -
9P ALA 3.4 1.6 - - - -
10P ASP* 1.3 79.7 - - - +
12P ARG* 1.3 58.8 + - - +
13P ILE* 3.2 14.3 + - - -
14P VAL* 4.5 12.8 - - - +
15P LYS* 4.5 8.9 - - - +
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Residues in contact with ARG 12 (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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1P MET* 3.4 28.6 - - - +
6P SER* 4.4 2.8 + - - -
7P GLU* 3.3 34.1 + - - +
10P ASP* 3.0 30.4 + - + +
11P GLY* 1.3 74.6 - - - +
13P ILE* 1.3 59.8 + - - +
14P VAL 3.6 0.7 - - - -
15P LYS* 3.8 30.9 - - - +
16P MET* 3.0 37.9 - - + +
53P GLN* 3.1 28.3 + - - -
56P THR* 3.4 10.9 + - + +
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Residues in contact with ILE 13 (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 ARG* 4.7 18.4 - - + +
11P GLY* 3.2 6.2 - - - -
12P ARG* 1.3 79.4 - - - +
14P VAL* 1.3 66.4 + - + +
17P GLU 3.6 1.7 + - - -
56P THR* 3.6 33.7 - - + +
59P ASP* 4.1 17.7 - - + +
60P MET* 3.6 35.8 - - + +
61P VAL* 3.3 26.0 - - - +
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Residues in contact with VAL 14 (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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11P GLY 4.5 9.4 - - - +
13P ILE* 1.3 76.1 - - + +
15P LYS* 1.3 64.8 + - + +
16P MET 3.0 2.2 - - - -
17P GLU* 2.8 25.4 + - + +
18P VAL* 3.0 19.4 + - + +
60P MET* 3.9 23.8 - - + -
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Residues in contact with LYS 15 (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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10P ASP* 6.0 3.0 - - - +
11P GLY 4.5 6.4 + - - +
12P ARG* 3.8 35.1 - - - +
13P ILE 3.6 0.2 - - - -
14P VAL* 1.3 81.1 - - + +
16P MET* 1.3 58.9 + - - +
18P VAL* 3.5 6.0 + - - +
19P ASP* 2.9 48.5 + - - +
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Residues in contact with MET 16 (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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12P ARG* 3.0 35.5 + - + +
14P VAL 3.0 0.6 - - - -
15P LYS* 1.3 77.8 - - + +
17P GLU* 1.3 54.2 + - - +
18P VAL 3.0 2.0 - - - -
19P ASP* 3.1 3.9 + - - +
20P TYR* 2.5 63.4 + - + +
53P GLN* 3.3 56.5 - - + +
56P THR* 3.3 17.5 - - - +
57P ALA* 4.1 19.3 - - + -
61P VAL* 3.8 13.2 - - + -
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Residues in contact with GLU 17 (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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13P ILE 3.6 2.7 + - - +
14P VAL* 2.8 15.2 + - - +
16P MET* 1.3 74.4 - - - +
18P VAL* 1.3 60.6 + - + +
20P TYR* 4.3 4.7 - - - +
21P SER* 2.9 30.6 + - - -
60P MET* 3.6 43.6 - - + +
61P VAL* 3.7 13.9 - - + +
64P SER* 3.7 24.5 + - - -
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Residues in contact with VAL 18 (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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14P VAL* 3.0 18.4 + - + +
15P LYS* 4.0 6.3 - - - +
17P GLU* 1.3 80.6 - - + +
19P ASP* 1.3 68.9 + - - +
20P TYR 3.3 0.9 - - - -
21P SER* 3.8 5.8 - - - -
22P ALA* 3.5 21.5 + - - +
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Residues in contact with ASP 19 (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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15P LYS* 2.9 38.5 + - - +
16P MET* 3.3 5.0 - - - +
18P VAL* 1.3 83.3 - - - +
20P TYR* 1.3 69.7 + - + +
22P ALA* 4.3 5.0 - - - +
23P THR* 2.9 22.5 + - - -
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Residues in contact with TYR 20 (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 MET* 2.5 53.4 + - + +
17P GLU* 3.8 6.6 - - - +
19P ASP* 1.3 82.3 - - + +
21P SER* 1.3 59.0 + - - +
22P ALA 3.6 0.4 - - - -
23P THR* 4.0 7.9 - - - -
24P VAL* 3.4 30.4 + - + +
50P LEU* 3.4 59.1 + - + +
52P LYS* 4.4 5.4 - - - -
53P GLN* 3.3 27.3 + - - +
57P ALA* 6.3 0.7 - - + -
61P VAL* 3.6 28.3 - - + -
65P ARG* 4.3 17.7 - - + -
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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