Contacts of the helix formed by residues 4 - 16 (chain G) in PDB entry 2W5J
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 LEU 4 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2F ASN* 4.2 19.6 - - + +
5F ILE* 3.5 28.8 - - + +
6F ALA 4.5 0.9 + - - -
2G ASN 4.3 2.7 - - - +
3G PRO* 1.3 84.0 - - - +
5G ILE* 1.3 71.9 + - + +
7G ALA* 4.1 0.2 - - - +
8G ALA* 3.3 24.6 + - - +
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Residues in contact with ILE 5 (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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5F ILE* 5.4 0.7 - - - -
2G ASN* 2.8 36.8 + - - +
4G LEU* 1.3 83.9 - - + +
6G ALA* 1.3 55.5 + - - +
7G ALA 3.0 1.9 + - - -
8G ALA* 3.2 2.8 + - - +
9G SER* 2.5 38.9 + - - -
4H LEU* 3.7 22.2 - - + +
5H ILE* 5.7 0.7 - - - -
8H ALA* 3.2 27.4 - - + -
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Residues in contact with ALA 6 (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 ASN* 2.4 28.6 + - + +
3G PRO* 5.1 0.9 - - + -
5G ILE* 1.3 74.9 - - - +
7G ALA* 1.3 60.9 + - - +
9G SER* 3.8 7.6 - - - -
10G VAL* 3.0 29.4 + - + +
3H PRO 4.8 1.8 - - - +
4H LEU 5.1 0.2 - - - +
7H ALA* 4.3 24.0 - - + -
8H ALA* 4.2 6.0 - - - +
11H ILE* 6.0 1.1 - - + -
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Residues in contact with ALA 7 (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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6F ALA* 4.1 14.6 - - + -
2G ASN 3.5 2.4 + - - -
3G PRO* 2.6 29.3 - - + +
4G LEU 4.1 0.2 - - - +
5G ILE 3.0 0.2 - - - -
6G ALA* 1.3 73.4 - - - +
8G ALA* 1.3 68.4 + - - +
9G SER 2.7 2.6 + - - -
10G VAL* 2.8 31.2 + - - +
11G ILE* 3.2 5.3 + - - +
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Residues in contact with ALA 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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5F ILE* 3.0 37.0 - - + -
6F ALA* 4.0 6.7 - - - +
9F SER* 2.8 36.9 + - - -
4G LEU 3.3 7.0 + - - +
5G ILE* 3.2 3.0 + - - +
7G ALA* 1.3 78.1 - - - +
9G SER* 1.3 62.1 + - - +
11G ILE* 3.2 2.0 + - - -
12G ALA* 2.9 16.6 + - - +
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Residues in contact with SER 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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5G ILE* 2.5 23.8 + - - -
6G ALA 3.6 5.2 - - - -
7G ALA 2.7 1.6 + - - -
8G ALA* 1.3 68.1 - - - +
10G VAL* 1.3 66.8 + - - -
11G ILE 2.9 0.7 + - - -
12G ALA* 3.1 5.0 + - - +
13G ALA* 2.8 26.5 + - - +
8H ALA* 3.0 32.5 + - - -
11H ILE* 2.8 23.0 - - - +
12H ALA* 4.0 3.1 + - - +
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Residues in contact with VAL 10 (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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6G ALA* 3.0 19.1 - - + +
7G ALA* 2.8 30.8 + - - +
9G SER* 1.3 76.3 - - - +
11G ILE* 1.3 61.1 + - + +
13G ALA* 4.2 0.2 - - - +
14G GLY* 2.6 32.4 + - - -
74G LEU* 3.7 26.4 - - - +
75G LEU* 5.4 9.7 + - + +
78G ASN* 4.2 11.9 - - + -
11H ILE* 3.3 38.4 - - + -
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Residues in contact with ILE 11 (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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6F ALA* 4.9 1.6 - - + +
9F SER* 2.8 27.1 - - - +
10F VAL* 3.1 47.8 - - + +
13F ALA* 3.3 14.1 - - + +
74F LEU* 4.0 16.8 - - + -
79F PRO* 5.1 4.5 - - + -
7G ALA 4.2 7.6 - - - +
8G ALA* 3.2 3.6 - - - +
9G SER 2.9 0.8 + - - -
10G VAL* 1.3 84.0 - - + +
12G ALA* 1.3 70.6 + - - +
14G GLY* 2.8 10.3 + - - -
15G LEU* 3.1 9.2 + - - +
75G LEU* 3.9 26.7 - - + -
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Residues in contact with ALA 12 (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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9F SER* 4.8 2.9 - - - +
12F ALA* 6.5 0.2 - - + -
13F ALA* 3.2 17.8 - - + +
8G ALA 2.9 16.1 + - - +
9G SER* 3.7 6.5 - - - +
11G ILE* 1.3 77.2 - - - +
13G ALA* 1.3 64.7 + - - +
14G GLY 2.9 0.2 + - - -
15G LEU* 3.1 10.0 + - - +
16G ALA* 3.2 11.8 + - - +
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Residues in contact with ALA 13 (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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9G SER 2.8 9.6 + - - +
10G VAL 4.2 0.2 - - - +
12G ALA* 1.3 73.8 - - - +
14G GLY* 1.3 60.3 + - - +
16G ALA* 3.5 10.9 + - - +
74G LEU* 6.0 1.8 - - + -
11H ILE* 3.1 40.6 - - + +
12H ALA* 3.5 23.3 - - + +
15H LEU* 2.7 31.5 - - + +
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Residues in contact with GLY 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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70F VAL* 5.5 3.4 - - - -
10G VAL 2.6 25.5 + - - -
11G ILE 2.8 3.0 + - - -
13G ALA* 1.3 77.5 - - - +
15G LEU* 1.3 55.3 + - - -
17G VAL* 2.9 25.9 + - - +
70G VAL 5.6 0.4 - - - -
71G ALA* 4.4 24.5 - - - +
74G LEU* 5.1 6.3 - - - +
75G LEU* 6.1 1.1 - - - -
15H LEU* 5.0 0.9 - - - -
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Residues in contact with LEU 15 (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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13F ALA* 2.6 39.0 - - + +
14F GLY* 4.8 0.9 - - - -
16F ALA* 3.1 18.7 - - + +
17F VAL* 3.3 20.2 - - + +
19F LEU* 5.3 0.2 - - - +
70F VAL* 5.3 10.2 - - + +
11G ILE 3.1 3.4 + - - +
12G ALA 3.1 7.2 + - - +
14G GLY* 1.3 68.0 - - - +
16G ALA* 1.3 55.7 + - - +
17G VAL 2.8 11.4 + - - -
18G GLY 3.1 12.4 + - - -
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Residues in contact with ALA 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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16F ALA* 5.0 4.6 - - + +
19F LEU* 5.8 0.9 - - - -
12G ALA 3.2 11.2 + - - +
13G ALA* 3.8 13.9 - - - +
14G GLY 3.1 1.4 + - - -
15G LEU* 1.3 73.4 - - - +
17G VAL* 1.3 65.4 + - - +
18G GLY 3.5 3.1 - - - +
19G LEU* 3.5 28.2 - - + +
15H LEU* 3.4 14.2 - - + +
16H ALA* 5.3 1.5 - - - +
18H GLY* 5.1 0.3 - - - -
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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