Contacts of the helix formed by residues 35 - 45 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31L GLU* 3.4 15.7 + - - -
34L ILE* 1.3 78.1 - - - +
36L ALA* 1.3 59.9 + - - +
37L GLU* 3.2 16.4 + - - +
38L ILE* 3.2 31.5 + - - +
39L MSE 2.9 25.3 + - - +
185L GLN* 2.6 21.6 + - - +
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Residues in contact with ALA 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L TYR* 3.2 30.2 - - + +
28L ASN* 3.6 23.3 - - + -
31L GLU* 3.0 14.5 + - - +
35L SER* 1.3 73.1 - - - +
37L GLU* 1.3 62.0 + - - +
39L MSE 3.7 1.1 - - - +
40L GLN* 3.0 29.6 + - - +
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Residues in contact with GLU 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187J LYS* 4.1 12.6 - - - -
35L SER* 3.6 13.2 + - - +
36L ALA* 1.3 81.7 - - - +
38L ILE* 1.3 62.7 + - - +
40L GLN* 4.1 3.0 - - - +
41L LEU* 3.3 27.6 + - + +
184L LEU* 3.7 39.0 - - + +
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Residues in contact with ILE 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L ILE* 4.0 13.2 - - + -
35L SER* 3.2 15.5 + - - +
37L GLU* 1.3 76.4 - - - +
39L MSE 1.3 68.4 + - - +
40L GLN 3.2 0.2 + - - -
41L LEU* 3.3 3.5 + - - +
42L HIS* 2.9 32.5 + - + +
180L HIS 3.8 16.1 - - - +
181L ALA* 3.5 20.6 - - - +
182L TYR* 3.7 20.4 - - - +
183L TYR 5.5 0.2 - - - +
184L LEU* 3.9 23.1 - - + +
185L GLN* 3.5 44.6 - - + +
186L TYR* 5.3 0.9 - - + -
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Residues in contact with MSE 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L LEU* 3.6 25.6 - - + -
25L TYR* 3.7 23.6 - - + +
27L TYR* 3.2 34.7 - - + +
30L LEU* 4.0 15.9 - - + -
34L ILE* 3.5 29.2 - - + +
35L SER 2.9 17.4 + - - +
36L ALA 3.7 1.3 - - - +
38L ILE* 1.3 77.6 - - - +
40L GLN* 1.3 57.2 + - - +
42L HIS* 3.8 6.0 - - - +
43L HIS* 3.1 29.8 + - - +
93L PHE* 5.9 0.7 - - - -
94L TRP* 3.7 30.1 - - + -
97L MSE 4.3 4.5 - - + -
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Residues in contact with GLN 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L TYR* 3.6 31.1 - - + +
36L ALA* 3.0 17.8 + - - +
37L GLU* 4.1 3.3 - - - +
39L MSE 1.3 73.0 - - - +
41L LEU* 1.3 63.6 + - + +
44L GLN* 2.9 65.0 + - - +
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Residues in contact with LEU 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183J TYR* 3.9 16.4 - - - +
187J LYS* 3.9 21.1 - - + -
188J ASN* 3.5 26.0 - - - +
37L GLU* 3.3 19.1 + - + +
38L ILE* 3.8 3.4 - - - +
40L GLN* 1.3 78.7 - - + +
42L HIS* 1.3 60.3 + - - +
45L LYS* 2.9 46.2 + - + +
46L HIS* 3.2 5.5 + - + -
180L HIS 5.9 0.7 - - - +
184L LEU* 3.4 33.9 - - + -
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Residues in contact with HIS 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L ILE* 2.9 23.1 + - - +
39L MSE 3.8 6.7 - - - +
41L LEU* 1.3 77.5 - - - +
43L HIS* 1.3 56.1 + - - +
46L HIS* 3.4 9.6 - - + +
47L HIS* 3.0 26.2 + - - +
90L HIS* 2.8 32.1 + + - -
93L PHE* 3.5 24.4 - + - -
94L TRP* 3.6 14.1 - + + -
176L ASP* 2.8 20.5 + - - -
180L HIS* 3.5 25.1 + + - +
181L ALA* 3.7 21.9 + - + -
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Residues in contact with HIS 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L LEU* 3.6 28.8 - - + +
21L PRO 2.8 27.2 + - - -
22L PRO* 4.4 3.6 - - + -
23L LEU* 3.4 38.5 - - + +
27L TYR* 2.6 33.0 + + + -
39L MSE 3.1 19.4 + - - +
42L HIS* 1.3 76.5 - - - +
44L GLN* 1.3 65.1 + - + +
47L HIS* 3.5 4.6 - - - +
48L GLN 3.2 20.4 + - - -
94L TRP* 3.7 19.3 - + + -
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Residues in contact with GLN 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L LEU* 4.7 5.2 - - + -
27L TYR* 3.6 25.6 + - - +
40L GLN* 2.9 50.5 + - - +
43L HIS* 1.3 78.7 - - + +
45L LYS* 1.3 75.7 + - + +
48L GLN* 3.1 22.5 - - - +
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Residues in contact with LYS 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188J ASN* 3.5 45.0 - - + +
41L LEU* 2.9 29.0 + - + +
44L GLN* 1.3 94.0 + - + +
46L HIS* 1.3 61.7 + - + +
47L HIS 3.7 0.2 - - - -
48L GLN* 3.7 1.6 + - - +
49L GLY* 2.9 25.7 + - - -
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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