Contacts of the helix formed by residues 4 - 16 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2J ASN* 4.4 19.1 - - + +
5J ILE* 3.6 28.2 - - + +
6J ALA 4.7 0.9 + - - -
2K ASN 4.4 2.2 - - - +
3K PRO* 1.3 84.3 - - - +
5K ILE* 1.3 72.5 + - + +
7K ALA* 4.1 0.2 - - - +
8K ALA* 3.4 21.8 + - - +
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Residues in contact with ILE 5 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J ILE* 5.6 0.4 - - - -
2K ASN* 2.8 40.3 + - - +
4K LEU* 1.3 79.9 - - + +
6K ALA* 1.3 57.2 + - - +
7K ALA 3.0 1.9 + - - -
8K ALA* 3.2 2.8 + - - +
9K SER* 2.5 38.1 + - - -
4L LEU* 3.2 27.1 - - + +
5L ILE* 5.2 1.1 - - - -
8L ALA* 2.8 37.0 - - + -
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Residues in contact with ALA 6 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K ASN* 2.4 28.7 + - + +
3K PRO* 5.1 0.7 - - + -
5K ILE* 1.3 75.3 - - - +
7K ALA* 1.3 57.1 + - - +
9K SER* 3.6 7.1 - - - -
10K VAL* 3.0 34.4 + - + +
3L PRO 4.6 1.8 - - - +
7L ALA* 3.9 25.8 - - + -
8L ALA* 4.2 5.8 - - - +
11L ILE* 5.7 1.1 - - + -
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Residues in contact with ALA 7 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J ALA* 4.2 14.6 - - + -
2K ASN 3.5 2.4 + - - -
3K PRO* 2.6 29.9 - - + +
4K LEU 4.1 0.2 - - - +
5K ILE 3.0 0.6 - - - -
6K ALA* 1.3 73.6 - - - +
8K ALA* 1.3 69.3 + - - +
9K SER 2.7 2.5 + - - -
10K VAL* 2.7 30.4 + - - +
11K ILE* 3.2 4.7 + - - +
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Residues in contact with ALA 8 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J ILE* 3.1 36.6 - - + -
6J ALA* 4.2 5.2 - - - +
9J SER* 2.9 34.7 + - - -
4K LEU 3.4 6.5 + - - +
5K ILE* 3.2 3.0 + - - +
7K ALA* 1.3 77.5 - - - +
9K SER* 1.3 58.0 + - - +
11K ILE* 3.1 3.1 - - - +
12K ALA* 2.9 23.1 + - - +
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Residues in contact with SER 9 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K ILE* 2.5 23.5 + - - -
6K ALA 3.6 4.5 - - - -
7K ALA 2.7 1.8 + - - -
8K ALA* 1.3 67.9 - - - +
10K VAL* 1.3 68.0 + - - -
11K ILE 2.9 0.7 + - - -
12K ALA* 3.1 6.1 + - - +
13K ALA* 2.7 23.9 + - - +
8L ALA* 2.8 35.8 + - - -
11L ILE* 2.6 33.3 - - - +
12L ALA* 3.8 3.0 + - - +
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Residues in contact with VAL 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K ALA* 3.0 18.6 - - + +
7K ALA* 2.7 30.4 + - - +
9K SER* 1.3 76.0 + - - +
11K ILE* 1.3 61.3 + - + +
13K ALA* 4.1 0.2 - - - +
14K GLY* 2.5 33.3 + - - -
74K LEU* 3.7 27.7 - - - +
75K LEU* 5.4 9.3 + - + +
78K ASN* 4.2 12.8 - - + -
79K PRO* 6.1 0.2 - - + -
11L ILE* 3.1 36.8 - - + -
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Residues in contact with ILE 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J ALA* 5.0 1.1 - - + +
9J SER* 2.8 26.7 - - - +
10J VAL* 3.2 38.6 - - + -
13J ALA* 3.1 23.7 - - + +
74J LEU* 4.0 14.8 - - + -
79J PRO* 5.4 3.4 - - + -
7K ALA 4.2 7.4 - - - +
8K ALA* 3.1 4.0 + - - +
9K SER 2.9 1.2 + - - -
10K VAL* 1.3 81.9 - - + +
12K ALA* 1.3 71.1 + - - +
14K GLY* 2.8 10.5 + - - -
15K LEU 3.1 9.0 + - - -
75K LEU* 3.9 27.8 - - + -
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Residues in contact with ALA 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J SER* 5.0 2.2 - - - +
13J ALA* 3.3 16.3 - - + +
8K ALA 2.9 14.4 + - - +
9K SER* 3.7 6.3 - - - +
11K ILE* 1.3 79.1 - - - +
13K ALA* 1.3 64.3 + - - +
14K GLY 2.9 0.2 + - - -
15K LEU* 3.0 11.1 + - - +
16K ALA* 3.2 11.4 + - - +
12L ALA* 6.5 0.4 - - + -
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Residues in contact with ALA 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K SER 2.7 8.0 + - - +
12K ALA* 1.3 73.4 - - - +
14K GLY* 1.3 60.8 + - - +
16K ALA* 3.5 10.4 + - - -
74K LEU* 6.0 1.1 - - + -
11L ILE* 3.0 54.7 - - + +
12L ALA* 3.4 12.0 - - - +
15L LEU* 2.5 32.4 - - + +
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Residues in contact with GLY 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70J VAL* 5.6 3.8 - - - -
10K VAL 2.5 25.3 + - - -
11K ILE 2.8 6.8 + - - -
13K ALA* 1.3 75.4 - - - +
15K LEU* 1.3 55.7 + - - -
17K VAL* 3.0 25.5 + - - +
70K VAL 5.6 0.2 - - - -
71K ALA* 4.4 24.7 - - - +
74K LEU* 5.1 5.8 - - - -
75K LEU* 6.2 1.8 - - - -
15L LEU* 4.9 0.4 - - - -
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Residues in contact with LEU 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J ALA* 2.5 39.7 - - + +
14J GLY* 4.9 0.7 - - - -
16J ALA* 3.2 18.8 - - + +
17J VAL* 3.2 21.8 - - + +
19J LEU* 5.2 0.5 - - - +
70J VAL* 5.5 7.5 - - + +
11K ILE 3.1 3.0 + - - -
12K ALA 3.0 5.9 + - - +
14K GLY* 1.3 68.9 - - - +
16K ALA* 1.3 54.9 + - - +
17K VAL* 2.8 11.8 + - - +
18K GLY 3.1 12.9 + - - -
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Residues in contact with ALA 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J ALA* 5.1 3.3 - - - +
19J LEU* 5.7 1.3 - - - -
12K ALA 3.2 10.5 + - - +
13K ALA* 3.8 14.6 - - - +
14K GLY 3.2 1.6 - - - -
15K LEU* 1.3 72.8 - - - +
17K VAL* 1.3 59.2 + - - +
18K GLY 3.5 2.2 - - - +
19K LEU* 3.7 26.6 - - + +
15L LEU* 3.1 24.2 - - + +
16L ALA* 5.5 2.2 - - + +
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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
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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