Contacts of the helix formed by residues 45 - 54 (chain D) in PDB entry 1RQF
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 HIS 45 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D VAL 3.8 0.2 + - - -
44D PRO* 1.3 91.1 - - + +
46D TYR* 1.3 65.2 + - - +
47D ARG 2.9 4.8 + - - -
48D GLN* 3.1 32.8 + - + +
49D ALA* 2.9 20.6 + - - +
68D GLN* 3.3 35.8 + - + +
71D LEU* 4.4 17.8 - - + +
72D ILE* 4.7 10.3 - - + -
75D ALA* 4.7 5.4 - - + -
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Residues in contact with TYR 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LEU* 3.4 15.2 - - + +
39D LEU* 4.5 1.6 - - + -
40D ASN* 2.9 69.3 + - + +
43D VAL* 3.7 28.7 + - + +
44D PRO 3.1 2.8 - - - -
45D HIS* 1.3 76.0 - - - +
47D ARG* 1.3 61.7 + - + +
49D ALA* 3.9 1.8 - - - -
50D LEU* 2.9 59.1 + - + +
79D LEU* 3.7 28.3 - - + -
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Residues in contact with ARG 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D HIS 2.9 2.2 + - - -
46D TYR* 1.3 87.2 - - + +
48D GLN* 1.3 94.3 + - + +
50D LEU* 3.3 3.3 + - - +
51D ASP* 2.7 42.6 + - - +
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Residues in contact with GLN 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D HIS* 3.1 32.3 + - + +
47D ARG* 1.3 111.8 - - - +
49D ALA* 1.3 57.4 + - - +
51D ASP* 3.3 9.9 + - - +
52D MET* 3.0 27.5 + - - +
68D GLN* 5.4 3.1 - - - +
72D ILE* 3.5 37.2 - - + +
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Residues in contact with ALA 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D VAL* 5.1 1.1 - - + -
44D PRO 4.5 0.4 - - - +
45D HIS* 2.9 17.8 + - + +
46D TYR* 3.9 2.5 - - - +
48D GLN* 1.3 75.5 - - - +
50D LEU* 1.3 64.9 + - - +
52D MET* 3.2 8.2 + - - +
53D ILE* 3.1 26.9 + - - +
72D ILE* 4.7 4.8 - - - +
75D ALA* 3.9 27.8 - - + +
76D ALA* 3.9 11.0 - - - +
79D LEU* 3.9 17.0 - - + -
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Residues in contact with LEU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ILE* 3.6 32.1 - - + +
36D LEU* 4.0 12.8 - - + -
46D TYR* 2.9 50.8 + - + +
47D ARG* 3.8 4.0 - - - +
49D ALA* 1.3 76.5 - - - +
51D ASP* 1.3 64.1 + - - +
53D ILE* 3.5 4.6 + - + -
54D LEU* 3.2 29.7 + - + +
79D LEU* 3.5 16.3 - - + +
83D ILE* 4.6 3.8 - - + -
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Residues in contact with ASP 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ARG* 2.7 38.9 + - - +
48D GLN* 3.4 12.6 - - - +
49D ALA 3.1 0.2 - - - -
50D LEU* 1.3 79.5 - - - +
52D MET* 1.3 56.7 + - - +
54D LEU 3.2 2.8 + - - -
55D ASP 3.0 24.1 + - - -
56D LEU* 3.1 49.4 + - + +
57D GLU 4.1 11.5 - - - +
58D PRO* 5.9 2.7 - - + -
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Residues in contact with MET 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D TRP* 3.3 34.3 - - + +
48D GLN 3.0 12.0 + - - +
49D ALA* 3.5 9.9 - - - +
51D ASP* 1.3 76.8 - - - +
53D ILE* 1.3 62.0 + - - +
55D ASP* 3.3 11.5 + - - +
56D LEU 5.1 2.9 - - - +
69D SER* 5.3 1.6 - - - +
72D ILE* 3.5 24.0 - - + -
73D GLU* 4.0 28.7 - - + -
76D ALA* 3.8 21.1 - - + -
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Residues in contact with ILE 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D TRP* 3.8 23.9 - - + +
10D ILE* 3.8 27.1 - - + +
30D ILE* 3.9 28.7 - - + -
49D ALA 3.1 9.2 + - - +
50D LEU* 3.8 8.3 - - + +
51D ASP 3.3 0.2 - - - -
52D MET* 1.3 77.1 - - - +
54D LEU* 1.3 63.0 + - + +
55D ASP* 3.3 3.5 + - - +
76D ALA* 3.6 16.2 - - + +
79D LEU* 3.5 38.6 - - + -
80D TYR* 3.6 24.7 - - + +
83D ILE* 4.1 5.4 - - + -
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ILE* 5.3 1.6 - - + -
27D GLU* 3.5 43.1 - - + +
30D ILE* 3.8 33.0 - - + +
31D GLN* 4.2 21.5 - - + +
50D LEU* 3.2 33.8 + - + +
51D ASP 3.2 4.4 + - - +
53D ILE* 1.3 80.0 - - - +
55D ASP* 1.3 73.7 + - - +
56D LEU* 3.6 23.4 - - + +
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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