Contacts of the helix formed by residues 31 - 41 (chain A) in PDB entry 1QXP
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 ASP 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LYS* 5.3 13.4 - - + +
29A ASN 3.9 2.8 + - - +
30A GLN* 1.3 77.7 - - - +
32A TYR* 1.3 64.5 + - - +
33A GLU* 2.7 31.5 + - - +
34A THR* 3.4 27.0 + - + +
35A LEU* 2.8 39.2 + - - +
153A VAL* 4.7 0.7 - - - -
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Residues in contact with TYR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLN 4.3 0.2 + - - -
31A ASP* 1.3 78.0 + - - +
33A GLU* 1.4 70.4 + - + +
35A LEU* 3.5 2.1 - - - +
36A ARG* 2.5 73.6 + - + +
128A GLY 4.0 8.7 + - - -
129A GLN* 3.6 21.2 - - + +
134A GLY 5.2 0.7 + - - -
135A TYR 5.6 0.3 + - - -
138A ILE* 2.7 49.7 + - + +
139A PHE* 4.0 5.5 - - - -
140A HIS* 3.6 41.7 - + + -
153A VAL* 3.3 27.1 - - + +
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Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ASP* 2.7 33.2 - - - +
32A TYR* 1.4 84.8 + - + +
34A THR* 1.4 56.5 - - - +
36A ARG* 2.9 20.1 + - - +
37A ASN* 2.9 46.8 + - - +
140A HIS* 5.2 3.9 + - - -
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Residues in contact with THR 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ASP* 3.4 28.8 + - + +
32A TYR 3.3 0.2 - - - -
33A GLU* 1.4 72.5 - - - +
35A LEU* 1.3 73.1 + - + +
37A ASN* 2.8 17.7 + - - +
38A GLU* 2.8 24.7 + - + +
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLN* 4.1 25.1 - - + +
31A ASP 2.8 23.9 + - - +
34A THR* 1.3 80.8 - - + +
36A ARG* 1.3 67.4 + - - +
37A ASN 2.8 0.9 + - - -
38A GLU* 3.1 33.8 + - - +
39A CYS* 3.3 17.0 + - - +
46A PHE* 3.4 41.7 - - + -
49A PRO* 5.6 4.3 - - + -
138A ILE* 3.5 21.5 - - + -
153A VAL* 4.3 5.8 - - + -
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Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TYR* 2.5 57.0 + - + +
33A GLU* 2.9 20.5 + - - +
35A LEU* 1.3 80.3 - - - +
37A ASN* 1.4 65.6 + - - +
39A CYS* 3.3 3.4 + - - +
40A LEU* 2.8 38.3 + - + +
128A GLY 5.3 3.6 + - - -
133A GLU* 5.4 4.9 + - - -
134A GLY* 3.1 31.1 + - - -
135A TYR 3.8 7.9 - - - +
136A ALA* 4.0 2.9 - - + -
138A ILE* 3.7 24.0 - - + -
491B GLU* 4.5 9.2 + - - -
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Residues in contact with ASN 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLU* 2.9 26.1 + - - +
34A THR* 2.8 10.5 + - - +
36A ARG* 1.4 86.8 + - - +
38A GLU* 1.3 58.7 + - - +
39A CYS 2.6 15.8 + - - -
40A LEU* 3.9 15.2 - - - +
41A GLU* 2.8 51.5 + - - +
430B THR* 5.3 7.7 + - - +
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Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A THR* 2.8 24.0 + - + +
35A LEU* 3.1 30.8 + - - +
37A ASN* 1.3 78.7 - - - +
39A CYS* 1.3 60.9 + - - +
41A GLU* 4.2 7.1 - - - +
42A ALA* 3.4 20.1 - - - +
44A ALA* 5.7 0.3 - - - +
46A PHE* 5.7 1.7 - - - -
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Residues in contact with CYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 3.3 11.4 + - - +
36A ARG 3.4 8.7 - - - +
38A GLU* 1.3 88.1 - - - +
40A LEU* 1.4 71.6 + - - +
42A ALA* 3.1 10.8 + - - -
43A GLY* 3.3 9.4 + - - -
44A ALA* 3.3 30.3 + - - +
45A LEU 4.1 0.7 - - - -
46A PHE* 3.5 47.8 - - - -
136A ALA* 4.0 12.8 - - + -
138A ILE* 5.6 0.2 - - - -
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG* 2.8 34.3 + - - +
37A ASN* 2.9 16.1 + - - +
39A CYS* 1.4 83.6 - - - +
41A GLU* 1.3 56.8 + - - +
42A ALA 2.8 5.5 + - - -
43A GLY* 3.5 6.1 + - - -
134A GLY* 4.4 9.4 - - - +
135A TYR* 4.7 2.0 - - + +
136A ALA* 4.1 19.1 - - + +
376B ASN* 5.3 3.5 + - - -
377B TYR* 4.7 12.8 - - - +
490B PHE* 3.7 24.4 - - + -
491B GLU* 3.0 30.5 - - + +
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Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ASN* 2.8 49.9 + - - +
38A GLU* 4.2 4.2 - - - +
39A CYS 3.9 0.2 - - - -
40A LEU* 1.3 70.4 - - - +
42A ALA* 1.3 62.5 + - - +
376B ASN* 6.1 0.9 - - - +
430B THR* 3.9 18.0 - - - +
465B HIS* 5.4 6.2 + - - +
466B PHE* 4.1 23.4 + - + +
467B ILE* 4.0 19.2 + - - +
490B PHE* 3.6 30.7 - - + -
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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