Contacts of the helix formed by residues 7 - 22 (chain A) in PDB entry 1L2L
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 TRP 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A GLU* 1.3 61.7 + - - +
9A SER* 3.2 4.2 - - - +
10A LEU* 3.1 33.3 + - + +
11A TYR* 2.9 35.8 + + + -
362A ARG* 4.3 5.6 - - - -
366A LEU* 4.3 14.6 - - + -
395A ILE* 3.2 26.0 - - + +
400A LEU* 6.1 3.4 - - + -
403A GLU* 2.8 39.1 + - - -
414A ASP* 3.6 20.9 - - - -
415A GLY* 3.8 12.6 - - - -
426A PHE* 3.2 24.7 - + - -
427A ILE* 3.6 20.0 - - + -
428A PRO* 3.4 31.5 - - + +
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Residues in contact with GLU 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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7A TRP* 1.3 79.0 - - - +
9A SER* 1.3 61.0 + - - +
11A TYR* 3.3 17.6 + - - +
12A GLU* 3.1 35.5 + - + +
391A LEU* 2.5 40.2 - - - +
393A VAL 5.1 2.8 - - - +
395A ILE* 4.2 13.0 - - + +
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Residues in contact with SER 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TRP* 3.2 2.3 - - - +
8A GLU* 1.3 75.1 - - - +
10A LEU* 1.3 70.4 - - - +
12A GLU* 3.2 11.1 + - - +
13A LYS* 3.0 49.7 + - - +
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TRP* 3.1 41.6 + - + +
9A SER* 1.3 79.8 - - - +
11A TYR* 1.3 57.1 + - - +
13A LYS* 3.9 16.8 - - + +
14A ALA* 2.9 31.7 + - - +
362A ARG* 4.3 24.7 - - - +
363A ASP* 5.5 0.2 - - - +
366A LEU* 3.5 16.1 - - + +
414A ASP* 4.5 27.4 - - + +
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Residues in contact with TYR 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 TRP* 2.9 29.6 + + + -
8A GLU* 3.4 23.8 - - - +
10A LEU* 1.3 77.8 - - - +
12A GLU* 1.3 61.1 + - - +
14A ALA* 3.8 1.3 - - - +
15A LEU* 3.2 23.7 + - - +
366A LEU* 3.5 46.4 - - + +
369A ALA* 3.5 20.4 - - + +
370A LEU* 3.5 40.5 - - + +
391A LEU* 4.9 3.8 - - + +
395A ILE* 4.4 16.4 - - + -
427A ILE* 3.7 3.2 - - + +
428A PRO 2.5 30.2 + - - -
429A THR* 3.7 6.5 - - - -
430A LYS* 4.2 2.4 + - - -
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Residues in contact with GLU 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 GLU* 3.1 30.4 + - - +
9A SER* 3.2 10.6 + - - +
11A TYR* 1.3 77.6 - - - +
13A LYS* 1.3 62.8 + - + +
15A LEU* 3.4 3.2 + - - +
16A ASP* 3.0 34.9 + - - +
388A ARG* 5.2 1.9 + - - +
391A LEU* 4.0 30.2 - - + +
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Residues in contact with LYS 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 SER* 3.0 36.2 + - - +
10A LEU* 3.9 16.7 - - + +
12A GLU* 1.3 74.1 - - + +
14A ALA* 1.3 66.6 + - - +
16A ASP* 3.4 10.6 + - - +
17A LYS* 3.1 30.3 + - + +
363A ASP* 5.4 0.4 - - - +
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Residues in contact with ALA 14 (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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10A LEU 2.9 19.4 + - - +
11A TYR 3.8 2.2 - - - +
13A LYS* 1.3 75.7 - - - +
15A LEU* 1.3 63.7 + - - +
17A LYS* 3.2 4.1 + - - +
18A VAL* 3.0 29.3 + - - +
363A ASP* 3.7 41.0 + - - +
366A LEU* 3.7 21.5 - - + -
367A PHE* 4.6 1.8 - - - +
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Residues in contact with LEU 15 (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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11A TYR 3.2 15.6 + - - +
12A GLU* 3.7 3.8 - - - +
14A ALA* 1.3 78.8 - - - +
16A ASP* 1.3 54.4 + - - +
18A VAL 3.4 0.3 + - - -
19A GLU* 2.7 47.0 + - + +
367A PHE* 3.9 19.3 - - + -
370A LEU* 3.6 17.0 - - + +
384A LEU* 5.3 3.4 - - + -
387A ILE* 3.8 36.1 - - + -
388A ARG* 3.2 41.5 - - + +
391A LEU* 4.1 12.8 - - + -
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Residues in contact with ASP 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 GLU* 3.0 28.0 + - - +
13A LYS* 3.6 9.0 - - - +
14A ALA 3.2 0.2 - - - -
15A LEU* 1.3 80.0 - - - +
17A LYS* 1.3 63.2 + - + +
19A GLU* 3.4 15.6 - - - +
20A ALA* 3.4 9.0 + - - +
388A ARG* 2.8 39.9 + - - +
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Residues in contact with LYS 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 LYS* 3.1 18.3 + - + +
14A ALA* 3.2 7.2 + - - +
16A ASP* 1.3 73.9 - - + +
18A VAL* 1.3 62.2 + - + +
20A ALA* 3.1 6.5 + - - +
21A SER* 2.8 33.7 + - - +
360A HIS* 4.7 13.4 + - - -
363A ASP* 3.7 28.7 - - - +
456A LEU* 4.4 14.4 - - + +
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Residues in contact with VAL 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 ALA 3.0 15.7 + - - +
15A LEU 4.0 0.4 - - - +
17A LYS* 1.3 73.4 - - + +
19A GLU* 1.3 68.7 + - - +
21A SER* 4.2 3.6 - - - +
22A ILE* 2.9 37.7 + - + +
363A ASP* 4.4 7.9 - - + +
367A PHE* 3.5 59.2 - - + -
384A LEU* 5.0 0.4 - - + +
452A SER* 3.7 21.1 - - - +
455A SER* 5.2 0.4 - - - +
456A LEU* 4.7 17.7 - - + -
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Residues in contact with GLU 19 (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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15A LEU* 2.7 28.5 + - + +
16A ASP* 3.4 10.1 - - - +
18A VAL* 1.3 78.9 - - - +
20A ALA* 1.3 61.2 + - + +
22A ILE* 4.7 2.8 + - - +
23A ARG* 5.9 3.1 + - - +
367A PHE* 5.2 0.4 - - - -
384A LEU* 3.0 46.8 - - + +
385A SER* 4.4 15.3 + - - -
388A ARG* 4.8 13.7 + - - +
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Residues in contact with ALA 20 (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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16A ASP 3.4 7.3 + - - +
17A LYS* 3.1 7.8 + - - +
19A GLU* 1.3 83.6 - - + +
21A SER* 1.3 61.4 + - - +
23A ARG* 4.7 17.5 + - - +
24A LYS* 5.0 3.1 - - - +
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Residues in contact with SER 21 (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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17A LYS* 2.8 17.4 + - - +
18A VAL* 4.4 0.4 - - - -
20A ALA* 1.3 81.5 - - - +
22A ILE* 1.3 66.6 + - - +
23A ARG 3.2 2.5 - - - -
24A LYS* 2.8 47.2 + - - +
455A SER* 3.4 8.0 - - - -
456A LEU* 3.6 27.3 - - - +
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Residues in contact with ILE 22 (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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18A VAL* 2.9 29.2 + - + +
19A GLU 4.8 2.2 - - - +
21A SER* 1.3 71.9 - - - +
23A ARG* 1.3 63.7 + - + +
24A LYS 3.0 4.9 + - - -
25A VAL* 3.4 14.0 + - - +
128A TYR* 3.3 59.0 - - + +
130A ILE* 3.6 19.6 - - + +
367A PHE* 4.1 20.2 - - + -
384A LEU* 3.9 18.4 - - + -
448A SER 5.1 0.7 - - - +
451A VAL* 4.4 4.7 - - + -
452A SER* 4.4 15.0 - - - +
455A SER* 3.6 9.7 + - - +
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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