Contacts of the helix formed by residues 2 - 20 (chain M) in PDB entry 6XXD
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 2 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1M PHE* 1.3 85.9 - - - +
3M LEU* 1.3 62.4 + - - +
4M ILE* 3.2 13.9 - - - +
5M GLU* 3.0 28.6 + - - +
6M LEU* 3.4 15.1 + - - +
1N PHE* 3.6 14.1 - - + -
5N GLU* 3.6 7.2 - - - +
9N VAL* 3.9 2.3 - - - +
20P LEU* 3.3 45.3 + - + +
21P ILE* 3.9 12.8 - - + -
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Residues in contact with LEU 3 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M THR* 1.3 72.9 - - - +
4M ILE* 1.3 54.9 + - - +
6M LEU* 3.2 13.6 + - + +
7M LEU* 2.7 44.9 + - + +
5N GLU* 2.9 32.0 + - + +
8N ILE* 4.1 21.8 - - + -
9N VAL* 3.6 20.4 - - + +
12N ILE* 5.7 2.5 - - + -
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Residues in contact with ILE 4 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M THR* 3.2 17.0 - - - +
3M LEU* 1.3 78.7 - - - +
5M GLU* 1.3 58.0 + - - +
7M LEU* 4.0 22.7 - - + -
8M ILE* 3.0 31.7 + - + +
21P ILE* 4.0 20.6 - - + -
22P PRO* 3.9 15.0 - - + -
24P LEU* 4.0 30.5 - - + -
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Residues in contact with GLU 5 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1L PHE 4.3 0.2 - - - +
2L THR* 3.6 6.4 - - - -
3L LEU* 2.9 42.6 + - + +
1M PHE* 3.2 41.1 - - - -
2M THR* 3.0 24.8 + - - +
4M ILE* 1.3 75.4 - - - +
6M LEU* 1.3 58.7 + - - +
8M ILE* 3.4 10.4 - - - +
9M VAL* 3.1 18.9 - - - +
20P LEU 5.1 1.3 - - - +
22P PRO* 3.9 21.8 - - + -
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Residues in contact with LEU 6 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1L PHE* 4.1 13.9 - - + +
1M PHE* 3.9 19.7 - - + -
2M THR 3.4 11.3 + - - +
3M LEU* 3.2 13.8 + - + +
5M GLU* 1.3 80.1 - - - +
7M LEU* 1.3 58.2 - - - +
9M VAL* 3.3 6.4 + - + +
10M ILE* 3.0 35.9 + - + +
9N VAL* 3.8 29.2 - - + +
12N ILE* 3.5 36.6 - - + -
13N ILE* 4.3 10.5 - - + -
16N LEU* 4.3 19.3 - - + -
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Residues in contact with LEU 7 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M LEU* 2.7 28.5 + - + +
4M ILE* 3.4 24.0 + - + +
6M LEU* 1.3 71.3 - - - +
8M ILE* 1.3 60.1 + - - +
10M ILE* 3.4 18.1 + - + +
11M ALA* 3.0 25.3 + - + +
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Residues in contact with ILE 8 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L LEU* 4.1 19.7 - - + -
4M ILE* 3.0 18.6 + - + +
5M GLU* 3.4 19.1 - - - +
7M LEU* 1.3 74.1 - - - +
9M VAL* 1.3 63.1 + - - +
11M ALA* 3.2 5.6 + - - +
12M ILE* 3.0 35.3 + - + +
22P PRO* 5.2 0.4 - - + -
24P LEU* 3.4 49.8 - - + +
27P ALA* 4.2 11.0 - - + -
28P ARG* 3.7 30.5 - - + +
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Residues in contact with VAL 9 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1L PHE* 3.5 43.3 - - + +
2L THR 3.9 0.7 - - - +
3L LEU* 3.6 40.4 - - + +
6L LEU* 3.8 12.3 - - + +
5M GLU* 3.1 20.6 + - - +
6M LEU* 3.3 11.4 + - + +
7M LEU 3.3 0.6 - - - -
8M ILE* 1.3 73.9 - - - +
10M ILE* 1.3 64.6 + - - +
12M ILE 3.5 0.7 + - - -
13M ILE* 3.1 28.9 + - + +
16N LEU* 5.4 4.0 - - + -
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Residues in contact with ILE 10 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6M LEU* 3.0 28.4 + - + +
7M LEU* 3.6 19.7 - - + +
8M ILE 3.3 0.2 - - - -
9M VAL* 1.3 75.5 - - - +
11M ALA* 1.3 61.9 + - - +
13M ILE* 3.5 9.1 + - - +
14M ALA* 3.3 21.0 + - - +
12N ILE* 4.1 24.5 - - + -
16N LEU* 4.1 22.2 - - + -
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Residues in contact with ALA 11 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M LEU* 3.0 13.2 + - + +
8M ILE* 3.2 13.4 + - - +
10M ILE* 1.3 78.3 - - - +
12M ILE* 1.3 59.8 + - - +
14M ALA* 3.5 8.2 + - - +
15M ILE* 3.3 26.7 + - - +
28P ARG* 4.1 20.9 - - - +
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Residues in contact with ILE 12 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L LEU* 5.7 3.6 - - + -
6L LEU* 3.5 29.6 - - + -
10L ILE* 4.1 5.8 - - + -
8M ILE* 3.0 23.7 + - + +
10M ILE 3.4 0.2 - - - -
11M ALA* 1.3 72.9 - - - +
13M ILE* 1.3 60.3 + - - +
15M ILE* 3.1 17.7 + - + +
16M LEU* 2.8 53.5 + - + +
27P ALA* 4.8 4.5 - - + +
28P ARG* 4.2 25.6 - - + +
31P ALA* 3.2 30.7 - - + -
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Residues in contact with ILE 13 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1K PHE 3.9 25.0 + - - +
1L PHE* 4.0 15.3 - - + -
6L LEU* 4.2 14.1 - - + -
9M VAL* 3.1 37.6 + - + +
10M ILE* 3.8 9.4 - - + +
11M ALA 3.4 0.2 - - - -
12M ILE* 1.3 74.8 - - - +
14M ALA* 1.3 57.3 + - - +
16M LEU* 4.1 5.7 - - - +
17M ALA* 2.9 34.3 + - + +
16N LEU* 4.9 5.6 - - + -
20N LEU* 4.0 28.5 - - + -
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Residues in contact with ALA 14 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M ILE 3.3 10.8 + - - +
11M ALA* 3.6 11.7 - - - +
12M ILE 3.2 0.2 - - - -
13M ILE* 1.3 80.1 - - - +
15M ILE* 1.3 60.9 + - + +
17M ALA* 3.8 4.6 + - - +
18M ALA* 3.5 20.4 + - - +
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Residues in contact with ILE 15 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M ALA 3.3 15.0 + - - +
12M ILE* 3.1 21.2 + - + +
14M ALA* 1.3 75.9 - - + +
16M LEU* 1.3 71.0 + - + +
18M ALA* 3.3 5.3 + - - +
19M VAL* 3.2 26.4 + - + +
28P ARG* 3.4 29.2 - - - +
31P ALA* 4.8 4.9 - - + +
32P ASN* 5.7 5.2 - - - +
35P VAL* 3.3 32.5 - - + -
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Residues in contact with LEU 16 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1K PHE* 4.4 22.3 - - + -
6L LEU* 4.3 13.7 - - + -
9L VAL* 5.4 1.6 - - + -
10L ILE* 4.1 19.3 - - + -
13L ILE* 4.9 5.2 - - + -
12M ILE* 2.8 43.7 + - + +
13M ILE* 4.1 3.1 - - - +
15M ILE* 1.3 82.9 - - + +
17M ALA* 1.3 60.9 + - - +
19M VAL* 4.1 6.7 - - + -
20M LEU* 3.2 50.6 + - + +
21M ILE* 4.4 0.3 - - - +
31P ALA* 4.7 7.2 - - + +
34P THR* 4.4 22.0 - - + +
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Residues in contact with ALA 17 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K PHE* 5.9 3.3 - - - +
13M ILE* 2.9 24.4 + - + +
14M ALA* 4.1 7.0 - - - +
15M ILE 3.3 0.2 - - - -
16M LEU* 1.3 76.1 - - - +
18M ALA* 1.3 57.8 + - - +
21M ILE* 3.3 32.2 - - + +
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Residues in contact with ALA 18 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M ALA 3.5 11.4 + - - +
15M ILE* 3.3 9.5 + - - +
16M LEU 3.2 0.6 - - - -
17M ALA* 1.3 81.5 - - - +
19M VAL* 1.3 67.5 + - + +
21M ILE* 3.8 14.2 + - - +
70P LYS* 4.6 13.7 + - - -
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Residues in contact with VAL 19 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M ILE* 3.2 19.0 + - + +
16M LEU* 4.0 4.7 - - + +
18M ALA* 1.3 79.7 - - + +
20M LEU* 1.3 78.8 + - + +
21M ILE 3.5 4.2 + - - +
34P THR* 4.4 3.6 - - + +
35P VAL* 4.0 40.2 - - + +
38P ALA* 3.9 26.0 - - + +
39P TYR 5.7 0.4 - - - +
42P ASP* 3.7 20.1 - - - +
70P LYS* 5.5 2.8 + - - +
73P PRO* 5.7 4.5 - - + -
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Residues in contact with LEU 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1J PHE 4.8 6.2 + - - +
2J THR* 3.4 26.8 + - + +
5J GLU* 5.1 1.6 - - - +
1K PHE* 3.4 34.5 - - + -
13L ILE* 4.0 22.0 - - + -
16M LEU* 3.2 34.7 + - + +
19M VAL* 1.3 77.7 - - + +
21M ILE* 1.3 64.0 + - + +
22M PRO* 3.3 8.9 - - - +
34P THR* 3.8 21.1 - - + -
38P ALA* 4.0 17.5 - - + -
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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