Contacts of the helix formed by residues 45 - 54 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A GLU* 3.0 22.8 + - - +
117A GLN* 3.8 24.9 - - - -
118A PRO* 4.1 19.3 - - + +
139A LYS* 4.8 7.2 + - - -
43J VAL 3.8 0.2 + - - -
44J PRO* 1.3 82.7 - - + +
46J TYR* 1.3 66.6 + - - +
47J ARG 2.9 5.0 + - - -
48J GLN* 3.1 25.9 + - - +
49J ALA* 2.9 19.3 + - - +
68J GLN* 4.4 14.7 + - - -
71J LEU* 4.0 39.2 - - + +
72J ILE* 4.2 17.0 - - + +
75J ALA* 4.4 3.1 - - + -
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Residues in contact with TYR 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A VAL* 3.5 28.4 + - - +
115A GLU* 3.5 28.8 - - + +
116A ASN* 2.7 34.8 - - + -
134B LYS* 5.1 5.2 + - - -
145B THR* 5.0 5.8 + - - -
40J ASN* 2.9 64.5 + - + +
43J VAL* 3.6 17.5 - - + +
44J PRO 3.1 2.0 - - - -
45J HIS* 1.3 77.0 - - - +
47J ARG* 1.3 62.0 + - + +
49J ALA* 4.0 2.4 - - - +
50J LEU* 3.0 25.3 + - - +
79J LEU* 4.0 0.5 - - - +
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Residues in contact with ARG 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A GLU* 2.8 47.2 + - + +
40J ASN* 4.9 0.9 - - - +
45J HIS 2.9 2.8 + - - -
46J TYR* 1.3 90.0 - - + +
48J GLN* 1.3 79.3 + - - +
50J LEU* 3.3 3.9 + - - +
51J ASP* 2.7 38.1 + - - +
59J ASP* 2.9 40.6 + - - +
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Residues in contact with GLN 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A GLU* 3.4 25.9 + - - +
45J HIS* 3.1 27.4 + - - +
47J ARG* 1.3 99.3 - - - +
49J ALA* 1.3 58.2 + - - +
51J ASP* 3.3 9.6 + - - +
52J MET* 2.9 28.1 + - - +
59J ASP* 4.4 14.4 - - + +
61J GLU* 4.3 4.7 - - - +
72J ILE* 2.8 45.7 - - + +
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Residues in contact with ALA 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J VAL* 5.1 0.7 - - + -
45J HIS 2.9 17.8 + - - +
46J TYR* 4.0 4.5 - - - +
48J GLN* 1.3 76.0 - - - +
50J LEU* 1.3 65.5 + - - +
52J MET* 3.3 3.3 + - - +
53J ILE* 3.1 27.4 + - - +
72J ILE* 4.1 5.8 - - - +
75J ALA* 3.6 17.3 - - + +
76J ALA* 3.4 32.3 - - - +
79J LEU* 4.2 8.5 - - + -
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Residues in contact with LEU 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J ILE* 3.6 32.1 - - + +
36J LEU* 4.0 22.7 - - + -
40J ASN* 4.4 13.9 - - - +
46J TYR 3.0 19.2 + - - +
47J ARG* 3.8 4.0 - - - +
49J ALA* 1.3 77.6 - - - +
51J ASP* 1.3 62.3 - - - +
53J ILE* 3.5 7.7 + - + -
54J LEU* 3.2 31.4 + - + +
79J LEU* 3.8 15.0 - - + +
83J ILE* 4.8 1.1 - - + -
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Residues in contact with ASP 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47J ARG* 2.7 33.9 + - - +
48J GLN* 3.4 11.2 - - - +
50J LEU* 1.3 81.0 - - - +
52J MET* 1.3 58.4 + - - +
54J LEU* 3.2 2.9 + - - -
55J ASP 3.0 24.3 + - - -
56J LEU* 3.1 49.2 + - + +
57J GLU 4.1 10.6 - - - +
58J PRO* 5.8 2.2 - - + -
59J ASP* 4.1 12.7 - - - +
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Residues in contact with MET 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J TRP* 3.3 36.7 - - + +
48J GLN 2.9 15.9 + - - +
49J ALA* 3.3 6.3 + - - +
51J ASP* 1.3 78.2 - - - +
53J ILE* 1.3 61.2 + - - +
55J ASP* 3.3 12.5 + - - +
56J LEU 5.1 2.2 - - - +
58J PRO* 6.2 4.5 - - + -
61J GLU* 6.0 0.2 - - - +
62J LEU* 4.8 17.3 - - + -
69J SER 5.0 0.2 - - - +
72J ILE* 3.9 18.8 - - + +
73J GLU* 3.7 44.0 - - + -
76J ALA* 3.9 11.7 - - + -
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Residues in contact with ILE 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J TRP* 3.7 26.9 - - + +
10J ILE* 3.8 29.4 - - + +
30J ILE* 4.0 22.2 - - + -
49J ALA 3.1 16.0 + - - +
50J LEU* 3.7 9.0 - - + +
51J ASP 3.2 0.2 - - - -
52J MET* 1.3 77.7 - - - +
54J LEU* 1.3 61.8 + - + +
55J ASP* 3.3 4.0 + - - +
76J ALA* 3.5 31.2 - - + +
79J LEU* 3.8 19.7 - - + -
80J TYR* 3.7 22.7 - - + +
83J ILE* 4.5 5.6 - - + -
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Residues in contact with LEU 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J ILE* 5.3 1.6 - - + -
27J GLU* 3.5 42.9 - - + +
30J ILE* 3.8 32.3 - - + +
31J GLN* 4.2 21.3 - - + +
50J LEU* 3.2 34.5 + - + +
51J ASP 3.2 4.7 + - - +
53J ILE* 1.3 79.4 - - - +
55J ASP* 1.3 75.5 + - - +
56J LEU* 3.7 25.5 - - + +
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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