Contacts of the helix formed by residues 26 - 37 (chain A) in PDB entry 2XQL
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 PRO 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A SER* 3.6 7.2 - - - +
24A GLN 3.5 0.8 - - - -
25A PHE* 1.3 87.4 - - + +
27A VAL* 1.3 66.2 + - - +
28A GLY 3.2 1.6 - - - +
29A ARG* 3.6 40.8 - - + +
30A VAL* 3.1 22.6 + - + +
52A ALA* 4.7 0.4 - - - -
37B TYR* 4.7 4.9 - - + -
40B TYR* 3.4 44.9 - - + +
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Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 3.6 33.9 - - + +
18A SER* 3.1 30.3 + - - +
23A LEU* 4.2 18.8 - - + -
25A PHE 3.1 6.8 + - - +
26A PRO* 1.3 71.2 - - - +
28A GLY* 1.3 59.0 + - - +
30A VAL* 3.1 4.9 + - - +
31A HIS* 2.8 27.3 + - - +
45A ALA 5.6 0.4 - - - +
48A PRO* 3.7 8.8 - - + +
49A VAL* 4.0 32.5 - - + +
52A ALA* 4.2 9.6 - - + -
121B TYR* 5.2 1.8 - - + -
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Residues in contact with GLY 28 (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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17A ARG* 3.3 28.0 + - - +
18A SER* 4.7 1.4 + - - -
26A PRO* 3.2 0.8 - - - +
27A VAL* 1.3 78.8 - - - +
29A ARG* 1.3 61.7 + - - +
31A HIS* 2.9 13.2 + - - +
32A ARG* 2.9 13.7 + - - +
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Residues in contact with ARG 29 (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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26A PRO* 3.4 32.4 + - + +
27A VAL 3.3 0.2 - - - -
28A GLY* 1.3 74.5 - - - +
30A VAL* 1.3 65.8 + - - +
32A ARG* 2.9 12.9 + - + +
33A LEU* 2.9 36.8 + - + +
36B SER* 2.6 47.8 + - - +
37B TYR* 3.9 23.1 - - - -
39B ILE* 6.2 0.6 - - - +
40B TYR* 3.7 21.2 + - - -
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Residues in contact with VAL 30 (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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25A PHE* 5.7 1.3 - - + -
26A PRO* 3.1 18.0 + - + +
27A VAL 3.5 7.2 - - - +
29A ARG* 1.3 79.5 - - - +
31A HIS* 1.3 62.0 + - - +
33A LEU* 3.4 7.2 + - - +
34A LEU* 3.0 46.8 + - + +
48A PRO* 3.7 25.8 - - + +
51A LEU* 4.0 10.3 - - + -
52A ALA* 4.1 17.5 - - + -
55A LEU* 4.3 14.8 - - + -
37B TYR* 4.7 11.4 - - + +
70B PHE* 4.0 10.5 - - + -
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Residues in contact with HIS 31 (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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17A ARG* 3.6 27.4 + - - +
27A VAL 2.8 12.7 + - - +
28A GLY 2.9 13.0 + - - +
30A VAL* 1.3 77.6 - - - +
32A ARG* 1.3 59.3 + - - +
34A LEU* 3.4 6.8 + - - +
35A ARG* 3.1 56.7 + - - +
43A VAL* 3.6 26.4 + - + +
44A GLY 3.8 7.2 + - - -
45A ALA* 4.9 4.0 - - - -
48A PRO* 3.2 37.6 - - + +
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Residues in contact with ARG 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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28A GLY 2.9 9.7 + - - +
29A ARG* 2.9 14.2 + - - +
31A HIS* 1.3 76.7 + - - +
33A LEU* 1.3 66.6 + - - +
35A ARG* 3.1 23.6 + - + +
36A LYS* 2.8 69.2 + - + +
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Residues in contact with LEU 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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29A ARG* 2.9 31.2 + - + +
30A VAL* 3.7 4.3 - - - +
32A ARG* 1.3 88.2 - - + +
34A LEU* 1.3 61.9 + - - +
36A LYS* 4.5 11.2 - - + -
37A GLY* 3.1 22.3 + - - -
39A TYR* 4.2 5.2 - - - -
37B TYR* 3.7 24.2 - - + +
67B ASN* 5.2 6.5 - - - +
70B PHE* 3.4 31.2 - - + -
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Residues in contact with LEU 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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30A VAL* 3.0 48.2 + - + +
31A HIS* 3.7 6.7 - - - +
32A ARG 3.2 0.4 - - - -
33A LEU* 1.3 79.2 - - - +
35A ARG* 1.3 61.6 + - - +
39A TYR* 3.8 27.9 + - + +
40A ALA 4.4 0.9 + - - -
43A VAL* 3.8 27.1 - - + +
47A ALA* 5.3 4.0 - - + -
48A PRO* 4.9 8.7 - - + -
51A LEU* 3.6 17.7 - - + -
70B PHE* 3.7 7.6 - - + -
74B ALA* 4.0 25.6 - - + -
89B ILE* 4.5 24.5 - - + -
94B ILE* 5.1 3.1 - - + -
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Residues in contact with ARG 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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31A HIS* 3.1 51.7 + - + +
32A ARG* 3.2 23.3 - - - +
34A LEU* 1.3 78.9 - - - +
36A LYS* 1.3 65.1 + - - +
38A ASN* 3.1 20.1 + - - -
40A ALA 4.9 6.1 - - - +
42A ARG* 6.4 0.7 - - - -
43A VAL* 4.1 14.1 - - + +
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Residues in contact with LYS 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 ARG* 2.8 63.1 + - + +
33A LEU* 4.2 10.8 - - + +
35A ARG* 1.3 72.6 - - - +
37A GLY* 1.4 54.8 + - - +
38A ASN* 2.9 28.4 + - - +
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Residues in contact with GLY 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 LEU 3.1 9.8 + - - -
36A LYS* 1.4 77.0 - - - +
38A ASN* 1.3 68.2 + - - +
39A TYR* 3.1 31.3 + - - -
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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