Contacts of the helix formed by residues 45 - 54 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43K VAL 3.8 0.2 + - - -
44K PRO* 1.3 88.8 - - + +
46K TYR* 1.3 65.4 + - - +
47K ARG 2.9 4.4 + - - -
48K GLN* 3.1 23.6 + - - +
49K ALA* 2.8 20.0 + - - +
71K LEU* 3.8 40.3 - - + +
72K ILE* 3.8 27.7 - - + +
75K ALA* 4.5 2.7 - - + -
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Residues in contact with TYR 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K LEU* 3.6 20.3 + - - +
39K LEU* 4.1 1.8 - - + -
40K ASN* 3.0 64.4 - - + +
43K VAL* 3.7 28.2 + - + +
44K PRO 3.1 3.0 - - - -
45K HIS* 1.3 75.6 - - - +
47K ARG* 1.3 64.0 + - + +
49K ALA* 3.9 2.4 - - - +
50K LEU* 3.0 58.6 + - + +
79K LEU* 3.6 23.6 - - + -
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Residues in contact with ARG 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45K HIS 2.9 2.2 + - - -
46K TYR* 1.3 87.1 - - + +
48K GLN* 1.3 95.0 + - + +
50K LEU* 3.8 3.0 - - - +
51K ASP* 2.6 42.9 + - - +
58K PRO 5.1 6.5 + - - -
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Residues in contact with GLN 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45K HIS* 3.1 27.6 + - - +
47K ARG* 1.3 110.6 - - - +
49K ALA* 1.3 58.0 + - - +
51K ASP* 3.3 9.2 + - - +
52K MET* 3.0 28.1 + - - +
58K PRO 4.9 11.2 - - - +
68K GLN* 5.7 0.9 + - - -
72K ILE* 2.7 42.7 - - + +
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Residues in contact with ALA 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43K VAL* 5.1 0.4 - - + -
45K HIS 2.8 17.4 + - - +
46K TYR* 3.9 6.1 - - - +
48K GLN* 1.3 76.3 - - - +
50K LEU* 1.3 65.6 + - - +
52K MET* 3.2 3.8 + - - +
53K ILE* 3.1 27.6 + - - +
72K ILE* 4.0 9.5 - - + +
75K ALA* 3.7 15.0 - - + +
76K ALA* 3.5 31.5 - - - +
79K LEU* 4.4 5.8 - - + -
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Residues in contact with LEU 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ILE* 3.6 32.1 - - + +
36K LEU* 4.0 13.2 - - + -
46K TYR* 3.0 51.3 + - + +
47K ARG* 3.8 4.0 - - - +
49K ALA* 1.3 76.1 - - - +
51K ASP* 1.3 63.5 + - - +
53K ILE* 3.5 8.1 + - + +
54K LEU* 3.2 29.8 + - + +
79K LEU* 3.9 15.8 - - + +
83K ILE* 4.8 1.1 - - + -
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Residues in contact with ASP 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47K ARG* 2.6 38.9 + - - +
48K GLN* 3.4 13.0 - - - +
49K ALA 3.1 0.4 - - - -
50K LEU* 1.3 77.4 - - - +
52K MET* 1.3 59.8 + - - +
54K LEU 3.2 2.6 + - - -
55K ASP 3.0 24.3 + - - -
56K LEU* 3.1 49.4 + - + +
57K GLU 4.1 10.8 - - - +
58K PRO* 5.1 6.2 - - + +
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Residues in contact with MET 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K TRP* 3.3 39.5 - - + +
48K GLN 3.0 13.4 + - - +
49K ALA* 3.5 9.4 - - - +
51K ASP* 1.3 77.7 - - - +
53K ILE* 1.3 60.1 + - - +
55K ASP* 3.3 12.2 + - - +
56K LEU 5.1 2.7 - - - +
69K SER* 5.4 3.1 - - - +
72K ILE* 4.2 15.7 - - + +
73K GLU* 3.9 41.3 - - + -
76K ALA* 4.2 7.4 - - + -
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Residues in contact with ILE 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K TRP* 3.8 23.7 - - + +
10K ILE* 3.8 27.7 - - + +
30K ILE* 3.9 29.6 - - + -
49K ALA 3.1 15.9 + - - +
50K LEU* 3.7 10.1 - - + +
51K ASP 3.3 0.2 - - - -
52K MET* 1.3 76.8 - - - +
54K LEU* 1.3 61.0 - - + +
55K ASP* 3.6 4.0 + - - +
76K ALA* 3.4 31.6 - - + +
79K LEU* 3.9 19.7 - - + -
80K TYR* 3.7 22.4 - - + +
83K ILE* 4.6 4.7 - - + -
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Residues in contact with LEU 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K ILE* 5.4 1.3 - - + -
27K GLU* 3.5 43.6 - - + +
30K ILE* 3.9 33.2 - - + +
31K GLN* 4.2 20.6 - - + +
50K LEU* 3.2 34.9 + - + +
51K ASP 3.2 4.6 + - - +
53K ILE* 1.3 81.0 - - - +
55K ASP* 1.3 72.0 + - - +
56K LEU* 3.7 23.3 - - + +
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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