Contacts of the helix formed by residues 2 - 20 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 3.4 45.6 + - + +
21A ILE* 3.9 12.3 - - + -
1F PHE* 1.3 84.7 - - - +
3F LEU* 1.3 62.4 + - - +
4F ILE* 3.2 13.8 - - - +
5F GLU* 3.0 28.9 + - - +
6F LEU* 3.4 15.1 + - - +
1G PHE* 3.6 14.6 - - + -
5G GLU* 3.6 6.7 - - - +
9G VAL* 3.9 2.6 - - - +
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Residues in contact with LEU 3 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F THR* 1.3 71.9 - - - +
4F ILE* 1.3 54.2 + - - +
6F LEU* 3.2 13.3 + - + +
7F LEU* 2.7 42.6 + - + +
5G GLU* 2.9 27.2 + - + +
8G ILE* 4.1 15.7 - - + -
9G VAL* 3.6 20.6 - - + +
12G ILE* 5.7 2.2 - - + -
22I PRO* 4.3 18.6 - - + -
23I ASN 5.2 1.6 - - - +
27I ALA* 4.4 26.0 - - + -
45L LYS* 4.1 28.7 - - + +
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Residues in contact with ILE 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 4.0 19.3 - - + -
22A PRO* 3.9 15.3 - - + -
24A LEU* 4.0 15.9 - - + -
2F THR* 3.2 17.2 - - - +
3F LEU* 1.3 79.4 - - - +
5F GLU* 1.3 59.0 + - - +
7F LEU* 4.0 8.5 - - + -
8F ILE* 3.0 29.3 + - - +
41L ASN* 5.0 4.0 - - - +
44L VAL* 4.1 15.3 - - + +
45L LYS* 3.8 38.9 - - + +
48L GLU* 3.7 30.3 - - + -
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Residues in contact with GLU 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU 5.2 1.3 - - - +
22A PRO* 4.0 20.4 - - + -
2E THR* 3.6 6.7 - - - -
3E LEU* 2.9 42.5 + - + +
1F PHE* 3.2 41.4 - - - -
2F THR* 3.0 24.6 + - - +
4F ILE* 1.3 76.0 - - - +
6F LEU* 1.3 59.1 + - - +
8F ILE* 3.4 10.2 - - - +
9F VAL* 3.1 19.4 - - - +
41K ASN* 5.9 1.0 + - - -
45K LYS* 4.5 9.0 - - - +
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Residues in contact with LEU 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E PHE* 4.1 14.4 - - + +
1F PHE* 3.9 18.8 - - + -
2F THR 3.4 10.5 + - - +
3F LEU* 3.2 14.5 + - + +
5F GLU* 1.3 79.4 - - - +
7F LEU* 1.3 58.2 + - - +
9F VAL* 3.3 7.1 + - + +
10F ILE* 3.0 36.5 + - + +
9G VAL* 3.8 29.8 - - + +
12G ILE* 3.5 36.8 - - + -
13G ILE* 4.2 11.4 - - + -
16G LEU* 4.3 18.6 - - + -
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Residues in contact with LEU 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F LEU* 2.7 26.1 + - + +
4F ILE* 3.4 10.7 + - + +
6F LEU* 1.3 71.3 - - - +
8F ILE* 1.3 60.9 + - - +
10F ILE* 3.4 12.0 + - + +
11F ALA* 3.0 25.5 + - - +
27I ALA* 5.6 8.1 - - - +
30I ARG* 4.3 21.8 - - + -
45L LYS* 3.4 47.3 - - + +
48L GLU* 4.6 7.6 - - + -
49L MET* 4.0 23.1 - - + -
52L ILE* 4.5 5.8 - - + +
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Residues in contact with ILE 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PRO* 5.3 0.2 - - + -
24A LEU* 3.4 49.8 - - + +
27A ALA* 4.2 10.8 - - + -
28A ARG* 3.7 18.2 - - + +
3E LEU* 4.1 19.5 - - + -
4F ILE* 3.0 16.4 + - - +
5F GLU* 3.4 18.4 - - - +
7F LEU* 1.3 74.2 - - - +
9F VAL* 1.3 64.6 + - - +
11F ALA* 3.2 5.4 + - - +
12F ILE* 3.0 34.5 + - + +
48L GLU* 3.5 24.0 - - + +
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Residues in contact with VAL 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E PHE* 3.4 43.1 - - + +
2E THR 3.9 0.4 - - - +
3E LEU* 3.6 40.2 - - + +
6E LEU* 3.8 12.7 - - + +
5F GLU* 3.1 22.2 + - - +
6F LEU* 3.3 11.1 + - + +
7F LEU 3.3 0.6 - - - -
8F ILE* 1.3 74.1 - - - +
10F ILE* 1.3 64.9 + - - +
12F ILE 3.5 0.5 + - - -
13F ILE* 3.1 29.1 + - + +
16G LEU* 5.4 4.0 - - + -
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Residues in contact with ILE 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F LEU* 3.0 28.1 + - + +
7F LEU* 3.6 16.4 - - + +
9F VAL* 1.3 74.6 - - - +
11F ALA* 1.3 62.3 + - - +
13F ILE* 3.5 9.4 + - + +
14F ALA* 3.3 21.2 + - + +
12G ILE* 4.1 24.7 - - + -
16G LEU* 4.1 19.1 - - + -
27I ALA 5.3 3.1 - - - +
30I ARG* 3.5 24.2 - - + +
31I ALA* 4.6 12.3 - - + +
34I THR* 3.2 24.2 + - - +
52L ILE* 5.4 3.4 - - + -
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Residues in contact with ALA 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 4.2 18.6 - - - +
7F LEU 3.0 10.5 + - - +
8F ILE* 3.2 13.0 + - - +
10F ILE* 1.3 78.0 - - - +
12F ILE* 1.3 61.1 + - - +
14F ALA* 3.5 6.7 + - - +
15F ILE* 3.3 25.8 + - - +
48L GLU* 4.8 3.6 - - + +
52L ILE* 3.2 40.1 - - + +
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Residues in contact with ILE 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 4.8 4.3 - - + +
28A ARG* 4.2 25.1 - - + +
31A ALA* 3.2 30.1 - - + -
3E LEU* 5.7 2.9 - - + -
6E LEU* 3.5 31.0 - - + -
10E ILE* 4.1 5.6 - - + -
8F ILE* 3.0 24.5 + - + +
9F VAL 3.5 0.2 + - - -
11F ALA* 1.3 72.8 - - - +
13F ILE* 1.3 60.0 + - - +
15F ILE* 3.1 17.2 + - + +
16F LEU* 2.8 53.8 + - + +
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Residues in contact with ILE 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D PHE 3.9 25.2 + - - +
1E PHE* 4.0 15.7 - - + -
6E LEU* 4.2 14.1 - - + -
9F VAL* 3.1 35.4 + - + +
10F ILE* 3.8 9.2 - - - +
11F ALA 3.4 0.4 - - - -
12F ILE* 1.3 75.2 - - - +
14F ALA* 1.3 58.5 + - - +
16F LEU* 4.1 5.7 - - - +
17F ALA* 2.9 33.9 + - + +
16G LEU* 4.9 6.1 - - + -
20G LEU* 4.0 21.3 - - + -
34I THR* 4.3 19.3 - - + -
37I THR* 6.1 2.9 - - + -
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Residues in contact with ALA 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ILE 3.3 10.8 + - - +
11F ALA* 3.6 11.7 - - - +
12F ILE 3.2 0.4 - - - -
13F ILE* 1.3 80.8 - - - +
15F ILE* 1.3 60.5 + - + +
17F ALA* 4.1 4.8 - - - +
18F ALA* 3.5 20.6 + - - +
37I THR* 5.6 7.0 - - + +
52L ILE* 4.9 14.4 - - + -
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Residues in contact with ILE 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 3.4 28.5 - - - +
31A ALA* 4.8 5.6 - - + +
32A ASN* 5.7 4.9 - - - +
35A VAL* 3.3 32.8 - - + -
11F ALA 3.4 14.6 - - - +
12F ILE* 3.1 21.6 + - + +
14F ALA* 1.3 76.8 - - + +
16F LEU* 1.3 71.2 + - + +
18F ALA* 3.3 5.5 + - - +
19F VAL* 3.2 25.5 + - + +
51L GLN 6.1 0.2 - - - +
52L ILE* 6.4 2.0 - - - -
55L ASN* 5.7 7.2 - - - +
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Residues in contact with LEU 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 4.7 6.1 - - + +
34A THR* 4.4 23.6 - - + +
1D PHE* 4.4 22.1 - - + -
6E LEU* 4.3 13.2 - - + -
9E VAL* 5.4 1.8 - - + -
10E ILE* 4.1 18.6 - - + -
13E ILE* 4.9 5.6 - - + -
12F ILE* 2.8 43.3 + - + +
13F ILE* 4.1 3.4 - - - +
15F ILE* 1.3 84.2 - - + +
17F ALA* 1.3 62.3 + - - +
19F VAL* 4.1 6.5 - - + -
20F LEU* 3.2 48.7 + - + +
21F ILE* 4.4 0.3 - - - +
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Residues in contact with ALA 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D PHE* 5.9 3.5 - - - +
13F ILE* 2.9 23.7 + - + +
14F ALA 4.1 4.0 - - - +
15F ILE 3.3 0.2 - - - -
16F LEU* 1.3 75.4 - - - +
18F ALA* 1.3 58.9 + - - +
21F ILE* 3.3 31.9 - - + +
37I THR* 4.0 26.9 - - + -
41I ASN* 5.8 7.4 - - + +
109I VAL* 4.7 10.1 + - + +
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Residues in contact with ALA 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LYS* 4.6 13.3 + - - -
14F ALA 3.5 10.8 + - - +
15F ILE* 3.3 9.8 + - - +
16F LEU 3.2 0.6 - - - -
17F ALA* 1.3 82.6 - - - +
19F VAL* 1.3 68.3 + - + +
20F LEU 3.6 0.2 - - - -
21F ILE* 3.8 13.7 - - - +
107I LYS 5.6 0.5 - - - +
109I VAL 4.6 13.2 - - - +
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Residues in contact with VAL 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A THR* 4.4 3.1 - - + +
35A VAL* 4.0 39.9 - - + +
38A ALA* 3.9 25.6 - - + +
39A TYR 5.7 0.4 - - - +
42A ASP* 3.7 20.1 - - - +
70A LYS* 5.5 2.7 + - - +
73A PRO* 5.8 4.7 - - + -
15F ILE* 3.2 19.3 + - + +
16F LEU* 4.0 4.0 - - + +
18F ALA* 1.3 80.1 - - + +
20F LEU* 1.3 78.7 + - + +
21F ILE 3.5 5.2 + - - +
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Residues in contact with LEU 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A THR* 3.9 21.5 - - + -
38A ALA* 4.0 17.0 - - + -
1C PHE 4.8 6.9 + - - +
2C THR* 3.4 26.4 + - + +
5C GLU* 5.1 1.4 - - - +
1D PHE* 3.4 35.2 - - + -
13E ILE* 4.0 21.3 - - + -
16F LEU* 3.2 34.5 + - + +
19F VAL* 1.3 78.4 - - + +
21F ILE* 1.3 64.3 + - + +
22F PRO* 3.3 8.3 - - - +
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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