Contacts of the helix formed by residues 35 - 45 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31V GLU* 3.7 12.1 - - - -
34V ILE* 1.3 74.7 - - - +
36V ALA* 1.3 59.6 + - - +
37V GLU* 3.6 7.7 + - - +
38V ILE* 3.2 30.0 + - - +
39V MSE 2.9 31.8 + - - +
184V LEU* 5.2 1.4 - - - +
185V GLN* 2.9 23.5 + - - +
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Residues in contact with ALA 36 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27V TYR* 3.3 19.0 - - + +
28V ASN* 3.6 31.9 - - + +
31V GLU* 3.1 13.2 + - - +
35V SER* 1.3 70.0 - - - +
37V GLU* 1.3 60.8 + - - +
39V MSE 3.7 0.9 - - - +
40V GLN* 2.9 33.2 + - - +
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Residues in contact with GLU 37 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35V SER* 3.2 7.8 + - - +
36V ALA* 1.3 76.7 - - - +
38V ILE* 1.3 66.1 + - - +
40V GLN* 3.3 5.1 + - - +
41V LEU* 2.9 35.7 + - + +
184V LEU* 3.5 28.1 - - + +
187X LYS* 3.4 22.9 - - - +
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Residues in contact with ILE 38 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34V ILE* 3.7 15.3 - - + -
35V SER* 3.2 26.7 + - - +
37V GLU* 1.3 79.3 - - - +
39V MSE 1.3 54.2 + - - +
41V LEU* 3.8 4.3 - - - +
42V HIS* 2.8 43.4 + - + +
180V HIS 3.7 17.6 - - - +
181V ALA* 3.6 20.2 - - - +
182V TYR* 3.9 17.0 - - - +
184V LEU* 3.7 21.8 - - + +
185V GLN* 3.7 35.2 - - + +
186V TYR* 5.3 0.9 - - + -
183X TYR* 6.1 0.7 - - + -
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Residues in contact with MSE 39 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23V LEU* 3.9 10.7 - - + +
25V TYR* 3.5 37.5 - - + +
27V TYR* 3.2 32.9 - - + +
30V LEU* 3.8 18.6 - - + -
34V ILE* 3.6 30.3 - - + +
35V SER 2.9 19.7 + - - +
36V ALA 3.7 0.9 - - - +
37V GLU 3.2 0.2 - - - -
38V ILE* 1.3 77.4 - - - +
40V GLN* 1.3 64.0 + - - +
42V HIS* 3.8 5.4 - - - +
43V HIS* 3.0 27.0 + - - +
93V PHE* 5.9 0.4 - - - -
94V TRP* 3.8 30.0 - - + -
97V MSE 4.6 0.9 - - - -
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Residues in contact with GLN 40 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27V TYR* 3.5 39.3 - - + +
36V ALA* 2.9 19.3 + - - +
37V GLU* 3.9 5.0 - - - +
39V MSE 1.3 76.0 - - - +
41V LEU* 1.3 56.3 + - + +
44V GLN* 2.8 72.1 + - - +
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Residues in contact with LEU 41 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37V GLU* 2.9 30.0 + - + +
38V ILE* 3.8 3.8 - - - +
40V GLN* 1.3 73.9 - - + +
42V HIS* 1.3 62.6 + - - +
44V GLN* 5.2 0.2 - - - -
45V LYS* 2.9 47.5 + - + +
46V HIS* 3.1 5.9 + - + -
180V HIS 5.9 0.2 - - - +
184V LEU* 3.5 31.9 - - + -
183X TYR* 3.8 20.0 - - + +
187X LYS* 4.0 17.3 - - + -
188X ASN* 3.5 24.0 - - - +
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Residues in contact with HIS 42 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34V ILE* 6.1 0.4 - - - +
38V ILE* 2.8 28.0 + - - +
39V MSE 3.8 5.2 - - - +
41V LEU* 1.3 73.2 - - - +
43V HIS* 1.3 57.7 + - - +
46V HIS* 3.4 9.7 - - + +
47V HIS* 2.8 27.2 + - - +
90V HIS* 2.8 24.5 + + - -
93V PHE* 3.7 22.3 - + - -
94V TRP* 3.5 14.9 - + + -
176V ASP* 2.7 30.7 + - - -
180V HIS* 3.6 22.3 + + - +
181V ALA* 3.5 25.3 + - + -
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Residues in contact with HIS 43 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V LEU* 3.4 30.9 - - + +
21V PRO 2.7 27.6 + - - -
22V PRO* 4.4 4.3 - - + -
23V LEU* 3.2 38.5 - - + +
27V TYR* 2.9 31.3 + + + -
39V MSE 3.0 18.9 + - - +
42V HIS* 1.3 75.8 - - - +
44V GLN* 1.3 64.4 + - + +
45V LYS 3.5 0.3 + - - -
47V HIS* 3.3 5.6 - - - +
48V GLN* 3.2 22.3 + - - +
94V TRP* 3.6 22.4 - - + -
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Residues in contact with GLN 44 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V LEU* 4.8 5.8 - - + -
27V TYR* 3.4 21.9 + - - +
40V GLN* 2.8 50.6 + - - +
43V HIS* 1.3 79.9 - - + +
45V LYS* 1.3 74.4 + - + +
48V GLN* 3.2 21.7 - - - +
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Residues in contact with LYS 45 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41V LEU* 2.9 35.8 + - + +
44V GLN* 1.3 91.1 + - + +
46V HIS* 1.3 59.5 + - - +
47V HIS 3.6 0.2 - - - -
48V GLN* 3.6 1.2 + - - +
49V GLY* 2.9 27.0 + - - -
188X ASN* 3.4 46.9 - - + +
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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