Contacts of the helix formed by residues 38 - 48 (chain A) in PDB entry 1QRY
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 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLN* 5.0 1.9 + - - -
36A TYR* 3.1 13.7 + - - -
37A LEU* 1.3 72.8 - - - +
39A ALA* 1.3 60.6 + - - -
40A PRO* 3.4 11.7 - - - -
41A GLU* 3.4 20.1 + - - +
42A ARG* 2.5 48.9 + - - +
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Residues in contact with ALA 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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38A SER* 1.3 83.8 - - - +
40A PRO* 1.3 71.0 - - + +
42A ARG* 3.6 7.1 - - - +
43A GLU* 3.6 23.2 + - - +
53A PRO* 4.9 5.2 - - - +
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Residues in contact with PRO 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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38A SER* 3.9 6.3 - - - -
39A ALA* 1.3 105.7 - - + +
41A GLU* 1.3 74.9 + - - +
43A GLU* 3.9 7.2 - - + +
44A HIS* 3.8 23.7 + - - -
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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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30A ARG* 4.4 14.8 + - - +
34A GLN* 3.3 38.9 + - + +
37A LEU* 3.8 11.9 - - + +
38A SER* 3.4 27.0 + - - +
39A ALA 3.6 0.2 - - - -
40A PRO* 1.3 87.2 - - - +
42A ARG* 1.3 71.5 + - - +
44A HIS* 3.2 28.8 + - - +
45A LEU 3.9 0.5 + - - -
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Residues in contact with ARG 42 (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 LEU* 2.4 61.6 + - + +
38A SER* 2.5 41.5 + - - +
39A ALA* 3.6 5.6 - - - +
41A GLU* 1.3 79.7 - - - +
43A GLU* 1.3 53.4 + - - +
45A LEU* 2.4 41.9 + - - +
46A THR* 4.2 2.7 - - - -
53A PRO* 2.9 39.9 - - + +
54A THR* 4.4 1.2 - - - +
56A VAL* 3.8 4.3 - - + -
57A LYS* 3.3 59.2 - - - +
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Residues in contact with GLU 43 (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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39A ALA 3.6 19.2 + - - +
40A PRO* 3.9 8.7 - - + +
42A ARG* 1.3 79.7 - - - +
44A HIS* 1.3 70.0 + - + +
45A LEU 2.9 0.3 - - - -
46A THR* 2.2 65.2 + - - +
47A SER* 3.0 3.9 + - - -
53A PRO* 3.3 25.6 - - + +
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Residues in contact with HIS 44 (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 ARG* 5.4 17.2 + - - +
40A PRO 3.8 12.7 + - - -
41A GLU* 3.2 24.7 + - - +
42A ARG 2.8 3.0 + - - -
43A GLU* 1.3 79.8 - - + +
45A LEU* 1.3 59.7 + - - +
47A SER* 3.0 24.8 + - - -
48A LEU* 3.4 8.5 - - - +
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Residues in contact with LEU 45 (chain A).
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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26A GLU* 4.3 3.6 - - + -
27A LEU* 3.5 28.5 - - + +
30A ARG* 4.1 25.9 - - + +
41A GLU 3.9 0.2 + - - -
42A ARG 2.4 21.9 + - - +
44A HIS* 1.3 66.0 - - - +
46A THR* 1.3 51.4 + - - +
47A SER 2.2 7.4 + - - -
48A LEU* 2.2 48.7 + - + +
49A ILE* 3.0 35.9 + - + -
51A LEU* 3.5 9.6 - - + +
56A VAL* 3.1 41.3 - - + -
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Residues in contact with THR 46 (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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43A GLU* 2.2 67.9 + - - -
45A LEU* 1.3 71.2 - - - +
47A SER* 1.3 57.1 + - - +
50A ARG* 3.0 32.9 - - - +
51A LEU 3.0 12.1 - - - +
52A THR* 4.6 2.0 - - - -
53A PRO* 2.7 50.7 - - + -
56A VAL* 3.8 2.5 - - + -
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Residues in contact with SER 47 (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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43A GLU* 3.0 5.2 + - - -
44A HIS* 3.0 17.3 + - - -
45A LEU 2.2 13.7 + - - -
46A THR* 1.3 72.1 + - - +
48A LEU* 1.3 76.6 + - - +
50A ARG* 4.5 3.6 + - - +
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Residues in contact with LEU 48 (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 GLU* 4.0 27.1 - - + +
44A HIS 3.4 12.1 - - - +
45A LEU* 2.2 32.4 + - + +
47A SER* 1.3 89.5 + - - +
49A ILE* 1.3 73.2 + - + +
50A ARG* 3.2 8.2 + - - +
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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