Contacts of the helix formed by residues 35 - 45 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31K GLU* 3.5 13.2 - - - -
32K PRO 5.0 1.3 - - - -
34K ILE* 1.3 77.0 - - - +
36K ALA* 1.3 62.8 + - - +
37K GLU* 3.8 10.5 + - - +
38K ILE* 3.1 31.4 + - - +
39K MSE 3.1 21.5 + - - +
184K LEU* 5.3 0.5 - - - +
185K GLN* 2.8 23.8 + - - +
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Residues in contact with ALA 36 (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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27K TYR* 3.1 30.0 - - + +
28K ASN* 3.6 23.1 - - + +
31K GLU* 3.0 15.4 + - - +
35K SER* 1.3 73.2 - - - +
37K GLU* 1.3 61.6 + - - +
39K MSE 3.5 2.1 + - - +
40K GLN* 3.1 26.6 + - - +
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Residues in contact with GLU 37 (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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187I LYS* 3.5 27.5 + - - +
35K SER* 3.1 8.8 + - - +
36K ALA* 1.3 77.1 - - - +
38K ILE* 1.3 65.4 + - - +
40K GLN* 3.3 6.8 + - - +
41K LEU* 3.0 30.1 + - + +
184K LEU* 3.7 34.3 - - + +
222N LEU* 5.8 0.3 - - - +
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Residues in contact with ILE 38 (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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34K ILE* 3.8 13.2 - - + -
35K SER* 3.1 24.7 + - - +
37K GLU* 1.3 77.1 - - - +
39K MSE 1.3 59.6 + - - +
41K LEU* 4.1 2.4 - - - +
42K HIS* 2.9 40.7 + - + +
180K HIS 4.0 10.4 - - - +
181K ALA* 3.4 27.1 - - - +
182K TYR* 3.5 35.0 - - - +
184K LEU* 3.9 22.9 - - + +
185K GLN* 3.6 23.3 - - + +
186K TYR* 5.2 0.9 - - + -
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Residues in contact with MSE 39 (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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23K LEU* 4.7 8.4 - - + +
25K TYR* 3.6 31.2 - - + -
26K ALA 5.6 0.7 - - - +
27K TYR* 3.1 37.7 - - + +
30K LEU* 3.6 20.2 - - + -
34K ILE* 3.6 30.5 - - + +
35K SER 3.1 17.0 + - - +
36K ALA 3.7 2.5 - - - +
37K GLU 3.3 0.2 - - - -
38K ILE* 1.3 78.4 - - - +
40K GLN* 1.3 56.1 + - - +
42K HIS* 3.9 5.0 - - - +
43K HIS* 3.1 30.0 + - - +
93K PHE* 5.7 0.9 - - - -
94K TRP* 3.5 36.0 - - + -
97K MSE 4.1 0.9 - - + -
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Residues in contact with GLN 40 (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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27K TYR* 3.4 44.7 - - + +
36K ALA 3.1 19.1 + - - +
37K GLU* 3.8 5.9 - - - +
39K MSE 1.3 75.0 - - - +
41K LEU* 1.3 62.2 + - + +
44K GLN* 2.9 58.0 + - - +
222N LEU* 5.6 11.2 - - - +
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Residues in contact with LEU 41 (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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183I TYR* 4.0 18.2 - - - +
187I LYS* 3.6 30.1 - - + +
188I ASN* 3.7 21.5 - - - +
37K GLU* 3.0 21.9 + - + +
38K ILE* 4.1 2.5 - - - +
40K GLN* 1.3 75.4 - - + +
42K HIS* 1.3 66.0 + - - +
45K LYS* 3.0 38.1 + - + +
46K HIS* 3.1 10.8 + - + -
180K HIS 6.1 0.4 - - - +
184K LEU* 3.4 33.9 - - + -
222N LEU* 6.5 1.1 - - + -
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Residues in contact with HIS 42 (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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38K ILE* 2.9 26.0 + - + +
39K MSE 3.9 6.1 - - - +
41K LEU* 1.3 77.1 - - - +
43K HIS* 1.3 57.5 + - - +
46K HIS* 3.3 10.9 - - + +
47K HIS* 2.9 27.2 + - - +
90K HIS* 2.7 29.7 + + - -
93K PHE* 3.5 22.0 - + - -
94K TRP* 3.6 15.4 - + + -
176K ASP* 2.9 18.9 + - - -
180K HIS* 3.3 24.7 + + - +
181K ALA* 3.5 27.0 - - + +
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Residues in contact with HIS 43 (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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20K LEU* 3.6 28.7 - - + +
21K PRO 3.0 26.3 + - - -
22K PRO* 4.5 3.1 - - + -
23K LEU* 3.6 37.7 - - + +
27K TYR* 4.0 14.2 + - + -
39K MSE 3.1 18.2 + - - +
40K GLN 3.9 1.3 - - - +
42K HIS* 1.3 78.9 - - - +
44K GLN* 1.3 69.6 + - - +
45K LYS 3.3 0.3 + - - -
47K HIS* 3.5 3.0 - - - +
48K GLN* 3.2 22.0 + - - +
94K TRP* 3.7 29.6 - - + -
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Residues in contact with GLN 44 (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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20K LEU* 4.8 6.3 - - + -
27K TYR* 2.9 28.5 + - - +
40K GLN* 2.9 40.0 + - - +
41K LEU* 5.2 0.2 - - - -
43K HIS* 1.3 81.1 - - + +
45K LYS* 1.3 80.6 + - + +
48K GLN* 3.0 23.9 - - - +
221N LYS* 5.6 2.0 - - - +
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Residues in contact with LYS 45 (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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188I ASN* 3.3 43.5 - - + +
41K LEU* 3.0 27.7 + - + +
44K GLN* 1.3 98.1 + - + +
46K HIS* 1.3 63.0 + - - +
48K GLN* 3.9 0.5 - - - +
49K GLY* 2.9 27.0 + - - -
221N LYS* 3.0 38.8 - - - +
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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