Contacts of the helix formed by residues 35 - 45 (chain E) in PDB entry 1P7G
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 SER 35 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27E TYR 4.2 0.2 - - - -
31E GLU* 3.6 13.7 - - - -
32E PRO 4.7 0.2 + - - -
34E ILE* 1.3 76.2 - - - +
36E ALA* 1.3 64.9 + - - +
37E GLU* 3.6 16.2 + - - +
38E ILE* 3.1 33.8 + - - +
39E MSE 3.0 20.3 + - - +
185E GLN* 2.8 22.7 + - - +
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Residues in contact with ALA 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E TYR* 2.9 30.2 + - + +
28E ASN* 3.5 22.2 - - + -
31E GLU* 3.7 13.1 + - - +
34E ILE 3.7 1.0 + - - -
35E SER* 1.3 72.9 - - - +
37E GLU* 1.3 61.5 + - - +
39E MSE 3.9 0.3 - - - +
40E GLN* 3.0 29.9 + - - +
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Residues in contact with GLU 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E SER* 3.6 13.3 + - - +
36E ALA* 1.3 80.4 - - - +
38E ILE* 1.3 59.2 + - - +
40E GLN* 4.2 4.2 - - - +
41E LEU* 3.4 25.7 + - + +
184E LEU* 3.3 42.0 - - + +
185E GLN* 5.9 0.2 - - - -
187G LYS* 3.6 22.4 + - - -
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Residues in contact with ILE 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ILE* 4.0 12.3 - - + -
35E SER* 3.1 21.8 + - - +
37E GLU* 1.3 75.4 - - - +
39E MSE 1.3 57.9 + - - +
41E LEU* 3.1 6.9 + - - +
42E HIS* 2.7 42.9 + - + +
180E HIS 3.7 21.5 - - - +
181E ALA* 3.9 13.9 - - - +
182E TYR* 4.0 17.5 - - - +
184E LEU* 3.9 20.9 - - + +
185E GLN* 3.5 38.8 - - + +
186E TYR* 5.5 0.7 - - + -
183G TYR* 6.2 0.9 - - + -
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Residues in contact with MSE 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E LEU* 3.7 10.3 - - + -
25E TYR* 3.5 32.8 - - + -
26E ALA 5.4 0.4 - - - +
27E TYR* 3.2 37.2 - - + +
30E LEU* 3.5 23.6 - - + -
34E ILE* 3.6 27.8 - - + +
35E SER 3.0 15.0 + - - +
38E ILE* 1.3 75.1 - - - +
40E GLN* 1.3 59.7 + - - +
42E HIS* 3.9 5.6 - - - +
43E HIS* 2.9 34.7 + - - +
93E PHE* 6.0 0.4 - - - -
94E TRP* 3.5 32.0 - - + -
97E MSE 4.6 1.1 - - - -
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Residues in contact with GLN 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E TYR* 3.6 22.7 - - + +
36E ALA* 3.0 18.5 + - - +
37E GLU* 4.2 4.3 - - - +
39E MSE 1.3 78.7 - - - +
41E LEU* 1.3 56.3 + - + +
44E GLN* 2.7 72.6 + - - +
222J LEU* 4.9 23.9 - - - +
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Residues in contact with LEU 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E GLU* 3.4 16.2 + - + +
38E ILE* 3.1 7.5 + - - +
40E GLN* 1.3 80.0 - - + +
42E HIS* 1.3 59.1 + - - +
45E LYS* 2.7 53.9 + - + +
46E HIS* 3.1 3.8 + - - -
180E HIS 6.0 0.4 - - - +
184E LEU* 3.7 24.9 - - + -
183G TYR* 3.6 24.2 - - + +
187G LYS* 3.9 22.9 - - + -
188G ASN* 3.7 24.7 - - - +
222J LEU* 6.6 0.2 - - + -
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Residues in contact with HIS 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ILE* 2.7 26.8 + - + +
39E MSE 3.9 5.4 - - - +
41E LEU* 1.3 74.4 - - - +
43E HIS* 1.3 57.3 + - - +
46E HIS* 3.5 9.3 - - + +
47E HIS* 2.9 26.9 + - - +
90E HIS* 2.6 29.2 + + - -
93E PHE* 3.8 20.0 - + - -
94E TRP* 3.6 13.9 - + + -
176E ASP* 2.8 27.2 + - - -
180E HIS* 3.3 33.8 + + - +
181E ALA* 3.8 15.9 - - + +
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Residues in contact with HIS 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E LEU* 3.5 30.2 - - + +
21E PRO 2.7 29.4 + - - -
22E PRO* 4.0 3.1 - - + -
23E LEU* 3.6 30.2 + - + -
27E TYR* 2.8 33.0 + - + -
39E MSE 2.9 19.0 + - - +
42E HIS* 1.3 77.8 - - - +
44E GLN* 1.3 61.5 + - + +
45E LYS 3.5 0.2 - - - -
47E HIS* 3.2 22.2 - - - +
48E GLN 3.6 1.2 + - - -
94E TRP* 3.5 38.8 - + + -
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Residues in contact with GLN 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E LEU* 4.9 5.4 - - + -
27E TYR* 2.7 49.3 + - - +
40E GLN* 2.7 49.0 + - + +
43E HIS* 1.3 77.2 - - + +
45E LYS* 1.3 64.8 + - + +
48E GLN* 3.3 20.9 - - - +
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Residues in contact with LYS 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E LEU* 2.7 44.1 + - + +
44E GLN* 1.3 81.2 - - + +
46E HIS* 1.3 64.3 + - + +
47E HIS 3.5 0.2 - - - -
48E GLN* 3.5 2.3 + - - +
49E GLY* 3.0 25.3 + - - -
188G ASN* 3.5 35.1 - - + +
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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