Contacts of the helix formed by residues 6 - 31 (chain A) in PDB entry 2L34
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 PRO 6 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A THR 4.9 0.2 - - - +
4A VAL* 4.1 8.0 - - + -
5A SER* 1.3 85.9 - - - +
7A GLY* 1.3 62.0 + - - +
8A VAL 3.5 1.1 - - - -
9A LEU* 3.3 25.8 - - + +
10A ALA* 3.3 9.0 + - - +
2B SER* 4.5 26.2 - - - +
6B PRO* 4.1 27.1 - - + -
9B LEU* 5.0 4.3 - - + +
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Residues in contact with GLY 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A SER* 3.0 6.4 - - - +
6A PRO* 1.3 76.6 - - - +
8A VAL* 1.3 66.3 + - - +
10A ALA* 2.9 19.3 + - - +
11A GLY* 3.1 9.0 + - - -
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Residues in contact with VAL 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A SER* 4.0 12.0 + - - +
7A GLY* 1.3 73.9 - - - +
9A LEU* 1.3 90.2 + - + +
11A GLY* 2.8 14.1 + - - +
12A ILE* 2.9 26.1 + - + +
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A SER 5.0 0.9 - - - +
6A PRO* 3.3 20.4 - - + +
7A GLY 3.1 0.2 - - - -
8A VAL* 1.3 98.8 - - + +
10A ALA* 1.3 58.4 + - - +
12A ILE* 2.8 24.1 + - + +
13A VAL* 3.1 13.9 + - - +
6B PRO* 4.8 8.7 - - + -
9B LEU* 3.6 44.1 - - + +
10B ALA* 3.8 7.2 - - + +
13B VAL* 3.3 31.4 - - + +
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PRO 3.3 7.8 + - - +
7A GLY* 2.9 13.1 + - - +
9A LEU* 1.3 77.5 - - - +
11A GLY* 1.3 63.1 + - - +
13A VAL* 3.2 27.1 + - + +
14A VAL* 3.2 15.8 + - + +
9B LEU* 3.8 5.3 - - + +
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Residues in contact with GLY 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLY 3.1 7.9 + - - -
8A VAL* 2.8 11.3 + - - -
10A ALA* 1.3 79.9 - - - +
12A ILE* 1.3 62.5 + - - +
14A VAL* 3.3 12.4 + - - +
15A GLY* 3.1 17.0 + - - -
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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
----------------------------------------------------------
8A VAL* 2.9 28.2 + - + +
9A LEU* 2.8 13.4 + - + +
11A GLY* 1.3 76.3 - - - +
13A VAL* 1.3 65.9 + - - +
15A GLY* 2.8 6.1 + - - -
16A ASP 2.8 17.7 + - - -
12B ILE* 5.1 0.2 - - + -
13B VAL* 3.3 43.7 - - + +
16B ASP* 3.5 16.2 - - + +
17B LEU* 6.2 0.7 - - + -
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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
----------------------------------------------------------
9A LEU 3.1 15.3 + - - +
10A ALA* 3.2 14.1 + - + +
12A ILE* 1.3 73.5 - - - +
14A VAL* 1.3 68.7 + - + +
16A ASP* 2.8 24.7 + - + +
17A LEU* 3.1 16.6 + - + +
9B LEU* 3.3 24.2 - - + -
12B ILE* 3.7 31.6 - - + -
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Residues in contact with VAL 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA* 3.2 15.2 + - + +
11A GLY* 3.3 11.9 - - - +
12A ILE 3.1 0.4 - - - -
13A VAL* 1.3 86.7 - - + +
15A GLY* 1.3 62.9 + - - +
17A LEU* 3.2 12.9 + - + +
18A VAL* 3.1 31.6 + - + +
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Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLY 3.1 10.0 + - - -
12A ILE* 2.8 10.2 + - - -
14A VAL* 1.3 77.0 - - - +
16A ASP* 1.3 56.4 + - - +
18A VAL* 3.2 12.5 + - - +
19A LEU* 2.9 33.2 + - - +
16B ASP* 3.6 5.6 - - - -
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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
----------------------------------------------------------
12A ILE 2.8 6.1 + - - +
13A VAL* 2.8 21.8 + - - +
15A GLY* 1.3 76.7 - - - +
17A LEU* 1.3 67.8 + - + +
19A LEU* 3.1 12.9 + - - +
20A THR* 3.0 19.3 + - - -
12B ILE* 4.6 10.1 - - + +
15B GLY 4.1 2.0 - - - +
16B ASP* 3.1 38.2 + - + +
19B LEU* 3.2 26.2 - - - +
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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
----------------------------------------------------------
13A VAL* 3.1 22.8 + - + +
14A VAL* 3.2 11.6 + - + +
16A ASP* 1.3 84.2 - - + +
18A VAL* 1.3 63.7 + - + +
20A THR* 3.3 6.9 + - - -
21A VAL* 3.1 32.0 + - + +
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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
----------------------------------------------------------
14A VAL* 3.1 23.8 + - + +
15A GLY* 3.3 13.7 - - - +
16A ASP 3.1 0.2 - - - -
17A LEU* 1.3 77.5 - - + +
19A LEU* 1.3 58.3 + - + +
21A VAL* 3.9 2.9 - - - +
22A LEU* 2.8 45.7 + - + +
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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
----------------------------------------------------------
15A GLY 2.9 14.0 + - - +
16A ASP* 3.1 7.4 + - - +
18A VAL* 1.3 75.9 - - + +
20A THR* 1.3 66.4 + - - +
22A LEU* 4.2 10.3 - - + -
23A ILE* 3.0 38.4 + - + +
16B ASP* 2.6 44.9 - - - +
19B LEU* 4.3 12.7 - - + +
20B THR* 2.9 38.4 - - + +
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Residues in contact with THR 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP* 3.0 16.7 + - - -
17A LEU* 3.6 9.4 - - - -
19A LEU* 1.3 77.2 - - - +
21A VAL* 1.3 56.6 + - + +
23A ILE* 4.7 0.2 - - - +
24A ALA* 2.7 42.8 + - + +
19B LEU* 3.0 29.4 - - + +
23B ILE* 4.6 7.1 - - + +
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Residues in contact with VAL 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.1 17.7 + - + +
18A VAL* 4.3 3.1 - - - +
20A THR* 1.3 78.2 - - + +
22A LEU* 1.3 60.5 + - - +
24A ALA* 4.2 4.3 - - - -
25A LEU* 2.9 41.5 + - + +
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 2.8 31.9 + - + +
19A LEU* 3.7 11.4 - - + +
21A VAL* 1.3 77.0 - - - +
23A ILE* 1.3 76.7 + - + +
25A LEU* 3.7 6.5 - - + +
26A ALA* 3.0 21.5 + - + +
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Residues in contact with ILE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.0 26.3 + - + +
22A LEU* 1.3 85.4 - - + +
24A ALA* 1.3 67.4 + - - +
26A ALA* 2.9 10.1 + - + +
27A VAL* 2.9 32.8 + - + +
20B THR* 5.1 15.7 - - + +
23B ILE* 3.1 46.2 - - + +
24B ALA* 4.5 10.3 - - + +
27B VAL* 4.8 4.5 - - + -
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A THR* 2.7 28.1 + - + +
21A VAL* 4.1 4.0 - - - +
23A ILE* 1.3 79.2 - - - +
25A LEU* 1.3 57.5 + - - +
27A VAL* 3.3 9.5 - - - +
28A TYR* 2.9 33.7 + - - +
23B ILE* 4.9 6.1 - - + +
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Residues in contact with LEU 25 (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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21A VAL* 2.9 30.2 + - + +
22A LEU* 3.7 7.6 - - + +
23A ILE 3.2 0.2 - - - -
24A ALA* 1.3 73.4 - - - +
26A ALA* 1.3 60.9 + - - +
28A TYR* 4.4 11.2 - - + -
29A PHE* 2.9 50.1 + - + +
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Residues in contact with ALA 26 (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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22A LEU* 3.0 15.3 + - + +
23A ILE* 2.9 16.3 + - + +
25A LEU* 1.3 78.5 - - - +
27A VAL* 1.3 65.4 + - + +
29A PHE* 3.8 2.9 - - - +
30A LEU 3.1 24.8 + - - +
31A GLY* 4.8 0.9 - - - -
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Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 2.9 22.8 + - + +
24A ALA* 3.3 17.5 - - - +
26A ALA* 1.3 71.2 - - + +
28A TYR* 1.3 81.6 + - + +
30A LEU* 3.9 0.2 - - - -
31A GLY* 3.0 30.9 + - - -
23B ILE* 4.7 6.5 - - + -
27B VAL* 3.1 35.2 - - + -
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Residues in contact with TYR 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA 2.9 16.7 + - - +
25A LEU* 4.1 12.8 - - + +
27A VAL* 1.3 87.0 - - + +
29A PHE* 1.3 69.1 + + - +
30A LEU* 4.5 0.2 - - - -
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Residues in contact with PHE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 2.9 33.4 + - + +
26A ALA* 3.8 3.8 - - - +
28A TYR* 1.3 86.3 - + - +
30A LEU* 1.3 81.1 + - + +
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA 3.1 8.2 + - - +
27A VAL 3.9 0.7 - - - -
28A TYR 3.4 0.2 - - - -
29A PHE* 1.3 101.6 - - + +
31A GLY* 1.3 65.1 + - - +
32A ARG* 2.8 35.9 + - - +
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Residues in contact with GLY 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA 3.7 1.3 + - - -
27A VAL* 3.0 34.0 + - - -
30A LEU* 1.3 71.8 - - - +
32A ARG* 1.3 52.5 + - - -
33A LEU* 2.5 26.2 + - - -
27B VAL* 5.9 3.1 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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