Contacts of the helix formed by residues 11 - 19 (chain K) in PDB entry 4M75
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 VAL 11 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10K SER* 1.3 80.3 - - - +
12K THR* 1.3 64.1 + - - +
13K THR 3.3 0.3 + - - -
14K GLU* 3.4 13.0 + - - +
15K PHE* 3.4 14.2 + - - +
35L VAL* 5.5 4.9 - - + +
36L GLY* 4.1 28.5 - - - +
37L PHE 4.6 6.5 + - - +
44L ILE* 4.3 12.7 - - + +
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Residues in contact with THR 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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10K SER 3.1 1.9 - - - +
11K VAL* 1.3 81.3 - - - +
13K THR* 1.3 62.1 + - - +
15K PHE* 3.5 3.1 + - - +
16K LEU* 3.2 33.9 + - - +
45K MSE 6.3 0.7 - - - -
38L ASP* 3.1 42.6 - - - +
42L ASN* 5.0 4.9 - - - -
44L ILE* 4.4 14.1 - - - +
72L LEU* 4.7 5.4 - - - +
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Residues in contact with THR 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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10K SER* 2.9 15.9 + - - +
12K THR* 1.3 81.1 - - - +
14K GLU* 1.3 63.0 + - - +
16K LEU* 3.2 18.4 + - - +
17K SER* 3.2 12.6 + - - -
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Residues in contact with GLU 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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10K SER 3.2 7.7 + - - +
11K VAL* 4.0 9.0 - - - +
12K THR 3.4 0.2 - - - -
13K THR* 1.3 78.4 - - - +
15K PHE* 1.3 52.5 + - - +
17K SER* 2.9 7.0 + - - -
18K ASP* 2.5 65.2 + - - +
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Residues in contact with PHE 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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11K VAL 3.4 9.0 + - - +
12K THR 3.7 8.3 - - - +
14K GLU* 1.3 77.0 - - - +
16K LEU* 1.3 55.5 + - - +
18K ASP* 2.7 25.9 + - + -
19K ILE* 2.7 55.9 + - + +
81K ILE* 3.7 22.7 - - + -
83K GLU* 4.5 9.4 - - + -
44L ILE* 4.3 17.0 - - + -
70L ARG* 4.0 52.5 - - + -
71L MSE 4.2 1.8 - - - -
72L LEU* 3.8 25.8 - - + -
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Residues in contact with LEU 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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12K THR* 3.2 24.1 + - - +
13K THR* 3.2 13.4 + - - +
14K GLU 3.1 0.2 - - - -
15K PHE* 1.3 81.6 - - + +
17K SER* 1.3 60.4 + - - +
19K ILE* 3.3 13.5 - - + +
20K ILE* 4.4 1.9 - - - +
41K ILE* 3.1 60.8 - - + +
42K ASP 4.7 10.5 - - - +
43K GLY* 5.9 3.8 - - - +
45K MSE 5.1 11.9 - - + -
81K ILE* 4.9 1.3 - - + -
72L LEU* 3.6 27.4 - - + -
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Residues in contact with SER 17 (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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13K THR 3.2 8.0 + - - -
14K GLU* 2.9 12.7 + - - -
16K LEU* 1.3 80.3 - - - +
18K ASP* 1.3 68.6 + - - +
20K ILE* 2.8 40.1 - - - +
41K ILE* 5.2 1.1 - - - -
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Residues in contact with ASP 18 (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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14K GLU* 2.5 58.4 + - - +
15K PHE* 2.7 18.1 + - + +
17K SER* 1.3 80.0 + - - +
19K ILE* 1.3 61.8 + - + +
20K ILE* 3.3 6.2 + - - +
22K LYS* 4.1 10.9 - - - +
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Residues in contact with ILE 19 (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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15K PHE* 2.7 53.9 + - + +
16K LEU* 3.3 23.1 - - + +
18K ASP* 1.3 74.6 - - + +
20K ILE* 1.3 52.4 + - - +
22K LYS* 2.7 47.0 + - + +
24K VAL* 3.9 22.7 - - + -
38K LEU* 3.0 31.6 - - + +
41K ILE* 4.4 10.3 - - + -
81K ILE* 4.5 11.4 - - + -
83K GLU* 4.2 12.6 - - + +
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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