Contacts of the helix formed by residues 1 - 20 (chain A) in PDB entry 5L26
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 MET 1 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-1A PRO 3.0 13.6 - - - +
0A ARG* 1.3 77.2 - - - +
2A VAL* 1.3 60.4 + - - +
3A VAL* 3.1 3.1 - - - -
4A LEU* 2.9 43.8 + - + +
5A HIS* 3.1 16.9 + - + +
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Residues in contact with VAL 2 (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 PRO 5.0 6.3 - - - -
0A ARG* 3.2 9.6 - - - +
1A MET* 1.3 82.1 - - - +
3A VAL* 1.3 50.1 + - + +
5A HIS* 3.2 8.7 + - + +
6A SER* 2.7 52.7 + - - +
413A GLY 4.0 19.7 - - - +
414A LEU* 4.1 13.0 - - + +
417A GLY* 5.1 11.7 - - - +
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Residues in contact with VAL 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A ARG* 3.2 27.1 - - + +
1A MET* 4.6 0.4 - - - -
2A VAL* 1.3 80.6 - - + +
4A LEU* 1.3 61.2 + - + +
6A SER* 4.3 0.2 - - - -
7A LEU* 2.9 44.4 + - + +
414A LEU* 3.7 25.1 - - + -
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Residues in contact with LEU 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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1A MET* 2.9 33.0 + - + +
3A VAL* 1.3 82.6 - - + +
5A HIS* 1.3 60.5 + - - +
7A LEU* 3.9 5.7 - - + +
8A LEU* 3.0 36.5 + - + +
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Residues in contact with HIS 5 (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 MET* 3.1 16.8 + - + +
2A VAL* 3.7 11.7 - - + +
4A LEU* 1.3 78.6 - - - +
6A SER* 1.3 61.5 + - - +
8A LEU* 3.6 16.3 - - + +
9A GLY 3.2 14.2 + - - -
308A TRP* 2.9 60.8 + + - -
309A VAL 3.7 12.6 + - - +
311A GLY* 3.8 23.5 + - - -
312A VAL 5.0 1.3 - - - -
313A PRO* 6.3 0.4 - - + -
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Residues in contact with SER 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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2A VAL* 2.7 33.8 + - - +
3A VAL 3.9 1.3 - - - -
5A HIS* 1.3 70.0 - - - +
7A LEU* 1.3 60.7 + - - +
8A LEU 3.1 1.1 - - - -
9A GLY 3.0 2.4 + - - -
10A MET* 2.8 32.5 + - - +
309A VAL 5.6 0.2 - - - -
310A ILE 5.5 3.9 + - - -
311A GLY* 6.0 1.8 - - - -
410A VAL* 3.3 19.8 + - - +
413A GLY 4.8 0.3 - - - -
414A LEU* 3.5 43.4 + - - +
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Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 2.9 32.9 + - + +
4A LEU* 4.1 6.7 - - + +
6A SER* 1.3 77.5 - - - +
8A LEU* 1.3 57.1 + - - +
10A MET* 3.6 27.4 - - + +
11A ALA* 2.9 29.3 + - - +
36A PHE* 5.4 3.8 - - + -
414A LEU* 5.9 3.6 - - + -
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Residues in contact with LEU 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 LEU* 3.0 25.7 + - + +
5A HIS* 3.6 20.2 - - + +
6A SER 3.1 0.2 - - - -
7A LEU* 1.3 76.9 - - - +
9A GLY* 1.3 60.3 + - - +
11A ALA* 3.1 7.6 + - - +
12A VAL* 2.9 47.2 + - + +
308A TRP* 4.9 15.5 - - + -
309A VAL* 4.3 12.8 - - + +
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Residues in contact with GLY 9 (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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5A HIS 3.2 4.8 + - - -
6A SER 3.0 7.4 + - - -
8A LEU* 1.3 79.6 - - - +
10A MET* 1.3 61.7 + - - +
12A VAL* 3.3 1.9 + - - +
13A LEU* 3.0 34.6 + - - +
309A VAL* 3.5 33.4 - - - +
310A ILE* 4.9 0.2 - - - -
410A VAL* 4.5 7.2 - - - -
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Residues in contact with MET 10 (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 SER* 2.8 17.5 + - - +
7A LEU* 3.6 27.6 - - + +
9A GLY* 1.3 76.5 - - - +
11A ALA* 1.3 60.9 + - - +
13A LEU* 3.4 1.9 + - - +
14A ILE* 3.1 32.4 + - + +
36A PHE* 3.6 33.9 - - + -
40A VAL* 4.6 9.4 - - + -
407A MET* 3.9 18.6 - - - -
410A VAL* 3.6 22.6 - - + +
411A ILE* 4.1 21.8 - - + -
414A LEU* 4.0 28.0 - - + -
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Residues in contact with ALA 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 LEU 2.9 19.2 + - - +
8A LEU* 3.1 8.3 + - - +
10A MET* 1.3 74.9 - - - +
12A VAL* 1.3 59.1 + - + +
14A ILE* 3.5 7.6 + - - +
15A ALA* 2.9 30.2 + - - +
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Residues in contact with VAL 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 LEU* 2.9 32.2 + - + +
9A GLY 3.7 5.2 - - - +
10A MET 3.3 0.2 - - - -
11A ALA* 1.3 77.3 - - + +
13A LEU* 1.3 59.2 + - + +
15A ALA* 3.1 7.2 + - + +
16A ILE* 2.9 52.4 + - + +
306A LEU* 5.8 2.7 - - + -
309A VAL* 4.0 27.8 - - + -
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLY 3.0 20.8 + - - +
10A MET 3.8 3.4 - - - +
12A VAL* 1.3 78.8 - - + +
14A ILE* 1.3 61.3 + - - +
16A ILE* 3.6 8.1 + - + +
17A ALA* 3.3 15.9 + - - +
216A PHE* 3.6 17.7 - - + -
306A LEU* 4.5 13.5 - - + -
309A VAL* 5.8 0.9 - - + -
310A ILE* 4.7 4.9 - - + -
403A LEU* 3.8 25.7 - - + +
406A LEU* 3.8 21.1 - - + -
407A MET* 3.6 48.5 - - + +
410A VAL* 3.7 17.0 - - + -
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Residues in contact with ILE 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 MET* 3.1 20.5 + - + +
11A ALA* 4.0 5.6 - - - +
13A LEU* 1.3 73.5 - - - +
15A ALA* 1.3 65.3 + - - +
17A ALA* 3.3 7.0 + - - +
18A VAL* 3.0 32.3 + - + +
36A PHE* 3.9 33.9 - - + -
215A LEU* 5.4 3.6 - - + -
216A PHE* 4.4 6.5 - - + -
219A LEU* 4.2 19.7 - - + -
407A MET* 4.0 10.8 - - + -
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Residues in contact with ALA 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 ALA 2.9 19.9 + - - +
12A VAL* 3.3 9.6 - - - +
14A ILE* 1.3 77.1 - - - +
16A ILE* 1.3 58.7 + - + +
18A VAL* 3.1 7.5 + - - +
19A LEU* 2.9 43.1 + - + +
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Residues in contact with ILE 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 VAL* 2.9 39.3 + - + +
13A LEU* 3.9 12.1 - - + +
15A ALA* 1.3 75.8 - - + +
17A ALA* 1.3 62.6 + - - +
19A LEU* 3.5 10.2 + - + +
20A LEU* 3.1 43.3 + - + +
306A LEU* 5.3 9.0 - - + -
399A VAL* 5.6 1.3 - - + -
403A LEU* 4.7 18.8 - - + -
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Residues in contact with ALA 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 LEU 3.3 6.1 + - - +
14A ILE 3.4 8.3 - - - +
15A ALA 3.1 0.4 - - - -
16A ILE* 1.3 78.9 - - - +
18A VAL* 1.3 63.0 + - - +
20A LEU* 3.1 2.6 + - - -
21A SER* 3.0 19.1 + - - -
216A PHE* 3.6 31.4 - - + -
219A LEU* 4.0 20.2 - - + +
220A LEU* 3.2 21.2 - - + +
403A LEU* 4.0 6.7 - - + +
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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 ILE* 3.0 25.3 + - + +
15A ALA* 3.7 6.1 - - - +
17A ALA* 1.3 75.7 - - - +
19A LEU* 1.3 66.4 + - + +
21A SER* 3.1 22.0 + - - -
24A ARG* 3.5 28.6 + - + -
27A ILE* 4.5 12.6 - - + -
219A LEU* 4.2 22.7 - - + -
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Residues in contact with LEU 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 ALA* 2.9 30.4 + - + +
16A ILE* 3.8 9.9 - - + +
18A VAL* 1.3 80.8 - - + +
20A LEU* 1.3 64.4 + - + +
21A SER 3.3 2.8 + - - +
24A ARG* 3.6 32.7 + - - +
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Residues in contact with LEU 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 ILE* 3.1 37.1 + - + +
17A ALA* 3.1 4.4 + - - -
19A LEU* 1.3 79.8 - - + +
21A SER* 1.3 65.5 + - - +
22A THR* 3.9 2.8 + - - +
220A LEU* 3.7 21.6 - - + +
396A LYS* 5.8 5.4 - - - +
399A VAL* 4.2 24.5 - - + -
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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
------------------------------------------------------------
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