Contacts of the helix formed by residues 2 - 20 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G PHE* 1.3 84.7 - - - +
3G LEU* 1.3 62.9 + - - +
4G ILE* 3.2 13.6 - - - +
5G GLU* 3.0 29.8 + - - +
6G LEU* 3.4 14.9 + - - +
1H PHE* 3.6 15.7 - - + -
5H GLU* 3.6 7.0 - - - +
9H VAL* 3.9 2.4 - - - +
20I LEU* 3.3 46.3 + - + +
21I ILE* 3.9 11.9 - - + -
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Residues in contact with LEU 3 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G THR* 1.3 72.0 - - - +
4G ILE* 1.3 56.6 + - - +
6G LEU* 3.2 12.8 + - + +
7G LEU* 2.7 42.2 + - + +
5H GLU* 2.9 25.7 + - + +
8H ILE* 4.1 15.9 - - + -
9H VAL* 3.6 19.7 - - + -
12H ILE* 5.7 2.7 - - + -
22J PRO* 4.3 18.4 - - + -
23J ASN 5.2 2.0 - - - +
27J ALA* 4.4 25.1 - - + -
45M LYS* 4.0 30.5 - - + +
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Residues in contact with ILE 4 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G THR* 3.2 17.3 - - - +
3G LEU* 1.3 79.8 - - - +
5G GLU* 1.3 59.2 + - - +
7G LEU* 4.0 9.2 - - + -
8G ILE* 3.0 29.0 + - - +
21I ILE* 4.0 19.3 - - + -
22I PRO* 3.9 15.0 - - + -
24I LEU* 4.0 16.6 - - + -
41M ASN* 5.0 4.0 - - - +
44M VAL* 4.1 15.5 - - + +
45M LYS* 3.8 38.6 - - + +
48M GLU* 3.7 30.3 - - + -
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Residues in contact with GLU 5 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F PHE 4.3 0.2 - - - +
2F THR* 3.6 6.4 - - - -
3F LEU* 2.9 42.6 + - + +
1G PHE* 3.2 41.8 - - - -
2G THR* 3.0 24.0 + - - +
4G ILE* 1.3 76.0 - - - +
6G LEU* 1.3 59.2 + - - +
8G ILE* 3.5 10.6 - - - +
9G VAL* 3.1 19.6 - - - +
20I LEU 5.1 1.6 - - - +
22I PRO* 3.9 20.6 - - + -
41L ASN* 5.9 0.7 + - - -
45L LYS* 4.5 9.4 - - - +
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Residues in contact with LEU 6 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F PHE* 4.1 14.6 - - + +
1G PHE* 3.9 19.7 - - + -
2G THR 3.4 11.1 + - - +
3G LEU* 3.2 14.6 + - + +
5G GLU* 1.3 79.2 - - - +
7G LEU* 1.3 57.6 + - - +
9G VAL* 3.3 6.7 + - + +
10G ILE* 3.0 36.0 + - + +
9H VAL* 3.8 29.8 - - + +
12H ILE* 3.5 36.3 - - + -
13H ILE* 4.2 10.5 - - + -
16H LEU* 4.3 18.8 - - + -
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Residues in contact with LEU 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G LEU* 2.7 26.3 + - + +
4G ILE* 3.4 10.7 + - + +
6G LEU* 1.3 70.9 - - - +
8G ILE* 1.3 59.5 + - - +
10G ILE* 3.4 12.8 + - + +
11G ALA* 3.0 24.4 + - - +
27J ALA* 5.6 8.1 - - + +
30J ARG* 4.3 20.9 - - + -
45M LYS* 3.4 47.1 - - + +
48M GLU* 4.5 7.9 - - + -
49M MET* 4.0 24.9 - - + -
52M ILE* 4.5 5.8 - - + +
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Residues in contact with ILE 8 (chain G).
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* 4.1 19.3 - - + -
4G ILE* 3.0 16.6 + - - +
5G GLU* 3.5 19.1 - - - +
7G LEU* 1.3 74.0 - - - +
9G VAL* 1.3 63.0 + - - +
11G ALA* 3.2 5.7 + - - +
12G ILE* 3.0 35.5 + - + +
22I PRO* 5.2 0.7 - - + -
24I LEU* 3.4 49.4 - - + +
27I ALA* 4.2 10.8 - - + -
28I ARG* 3.7 18.2 - - + +
48M GLU* 3.5 23.1 - - + +
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Residues in contact with VAL 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F PHE* 3.4 43.3 - - + +
2F THR 4.0 0.4 - - - -
3F LEU* 3.6 41.1 - - + +
6F LEU* 3.8 13.3 - - + +
5G GLU* 3.1 20.9 - - - +
6G LEU* 3.3 11.5 + - + +
7G LEU 3.3 0.4 - - - -
8G ILE* 1.3 73.5 - - - +
10G ILE* 1.3 65.7 + - - +
12G ILE 3.5 0.3 + - - -
13G ILE* 3.1 29.7 + - + +
16H LEU* 5.4 3.8 - - + -
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Residues in contact with ILE 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G LEU* 3.0 28.1 + - + +
7G LEU* 3.6 15.5 - - + +
8G ILE 3.3 0.2 - - - -
9G VAL* 1.3 75.2 - - - +
11G ALA* 1.3 62.6 + - - +
13G ILE* 3.5 9.6 + - + +
14G ALA* 3.3 20.8 + - + +
12H ILE* 4.1 24.5 - - + -
16H LEU* 4.1 19.7 - - + -
27J ALA 5.3 3.1 - - - +
30J ARG* 3.5 24.9 - - + +
31J ALA* 4.6 12.6 - - + +
34J THR* 3.2 24.6 + - - +
52M ILE* 5.4 2.2 - - + -
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Residues in contact with ALA 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G LEU 3.0 11.6 + - - +
8G ILE* 3.2 12.9 + - - +
10G ILE* 1.3 77.5 - - - +
12G ILE* 1.3 61.2 + - - +
14G ALA* 3.5 6.9 + - - +
15G ILE* 3.3 26.3 + - - +
28I ARG* 4.1 18.8 - - - +
48M GLU* 4.8 3.4 - - + +
52M ILE* 3.3 39.0 - - + +
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Residues in contact with ILE 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F LEU* 5.7 3.1 - - + -
6F LEU* 3.5 30.3 - - + -
10F ILE* 4.1 6.1 - - + -
8G ILE* 3.0 25.3 + - + +
10G ILE 3.4 0.2 - - - -
11G ALA* 1.3 73.7 - - - +
13G ILE* 1.3 61.4 + - - +
15G ILE* 3.1 17.7 + - + +
16G LEU* 2.8 52.9 + - + +
27I ALA* 4.7 4.7 - - + +
28I ARG* 4.2 24.5 - - + +
31I ALA* 3.2 30.5 - - + -
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Residues in contact with ILE 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E PHE 3.9 23.9 + - - +
1F PHE* 4.0 16.2 - - + -
6F LEU* 4.2 16.4 - - + -
9G VAL* 3.1 36.7 + - + +
10G ILE* 3.8 9.2 - - - +
11G ALA 3.4 0.2 - - - -
12G ILE* 1.3 74.8 - - - +
14G ALA* 1.3 57.3 + - - +
16G LEU* 4.1 5.1 - - - +
17G ALA* 2.9 33.9 + - + +
16H LEU* 4.9 5.8 - - + -
20H LEU* 4.0 20.9 - - + -
34J THR* 4.3 20.4 - - + -
37J THR* 6.1 3.4 - - + -
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Residues in contact with ALA 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ILE 3.3 10.2 + - - +
11G ALA* 3.6 11.0 - - - +
12G ILE 3.2 0.6 - - - -
13G ILE* 1.3 79.9 - - - +
15G ILE* 1.3 60.4 + - + +
17G ALA* 3.8 5.3 + - - +
18G ALA* 3.5 20.4 + - - +
37J THR* 5.6 7.4 - - - +
52M ILE* 4.9 14.6 - - + -
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Residues in contact with ILE 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ALA 3.3 15.0 + - - +
12G ILE* 3.1 21.2 + - + +
14G ALA* 1.3 75.7 - - + +
16G LEU* 1.3 72.5 + - + +
18G ALA* 3.3 5.5 + - - +
19G VAL* 3.2 26.3 + - + +
28I ARG* 3.4 28.7 - - - +
31I ALA* 4.8 4.7 - - + +
32I ASN* 5.7 4.7 - - - +
35I VAL* 3.3 32.8 - - + -
51M GLN 6.1 0.4 - - - +
52M ILE* 6.5 2.2 - - - -
55M ASN* 5.7 7.6 - - - +
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Residues in contact with LEU 16 (chain G).
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* 4.4 22.2 - - + -
6F LEU* 4.3 13.7 - - + -
9F VAL* 5.4 1.3 - - + -
10F ILE* 4.1 18.6 - - + -
13F ILE* 4.9 5.4 - - + -
12G ILE* 2.8 44.3 + - + +
13G ILE* 4.1 3.1 - - - +
15G ILE* 1.3 83.8 - - + +
17G ALA* 1.3 60.3 + - - +
19G VAL* 4.1 5.6 - - + -
20G LEU* 3.2 49.8 + - + +
21G ILE* 4.4 1.2 - - - +
31I ALA* 4.7 7.6 - - + +
34I THR* 4.3 21.5 - - + +
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Residues in contact with ALA 17 (chain G).
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* 5.9 3.7 - - - +
13G ILE* 2.9 24.2 + - + +
14G ALA 4.1 4.0 - - - +
16G LEU* 1.3 75.8 - - - +
18G ALA* 1.3 59.2 + - - +
21G ILE* 3.3 31.6 - - + +
37J THR* 4.0 26.9 - - + -
41J ASN* 5.8 7.4 - - + +
109J VAL* 4.7 11.0 + - + +
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Residues in contact with ALA 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G ALA 3.5 11.4 + - - +
15G ILE* 3.3 9.6 + - - +
16G LEU 3.2 0.4 - - - -
17G ALA* 1.3 80.6 - - - +
19G VAL* 1.3 68.2 + - + +
20G LEU 3.6 0.4 + - - -
21G ILE* 3.8 14.0 - - - +
70I LYS* 4.6 14.1 + - - -
107J LYS 5.6 0.2 - - - +
109J VAL 4.6 13.0 - - - +
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Residues in contact with VAL 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G ILE* 3.2 19.2 + - + +
16G LEU* 4.0 4.5 - - + +
18G ALA* 1.3 79.1 - - + +
20G LEU* 1.3 78.3 + - + +
21G ILE 3.5 4.7 + - - +
34I THR* 4.4 3.8 - - + +
35I VAL* 4.0 40.8 - - + +
38I ALA* 3.9 25.0 - - + +
39I TYR 5.7 0.2 - - - +
42I ASP* 3.7 20.1 - - - +
70I LYS* 5.5 2.8 + - - +
73I PRO* 5.7 4.5 - - + -
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Residues in contact with LEU 20 (chain G).
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 4.8 6.5 - - - +
2D THR* 3.3 27.0 + - + +
5D GLU* 5.1 1.4 - - - +
1E PHE* 3.4 34.8 - - + -
13F ILE* 4.0 22.4 - - + -
16G LEU* 3.2 35.0 + - + +
19G VAL* 1.3 77.7 - - + +
21G ILE* 1.3 62.9 + - - +
22G PRO* 3.3 8.3 - - - +
34I THR* 3.8 22.0 - - + +
38I ALA* 4.0 17.0 - - + -
42I ASP* 6.1 0.2 - - - -
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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