Contacts of the helix formed by residues 53 - 64 (chain A) in PDB entry 1RQG
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 GLY 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A TYR* 3.3 6.6 + - - -
52A HIS* 1.3 80.3 - - - +
54A THR* 1.3 66.1 + - - -
55A PRO* 3.4 4.7 - - - -
56A ILE* 3.8 1.2 + - - +
57A SER* 3.1 19.4 + - - -
233A LEU* 3.6 13.6 - - - +
235A TRP* 4.6 3.8 + - - -
252A TYR* 6.1 0.2 - - - -
253A VAL* 3.8 23.8 - - - +
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Residues in contact with THR 54 (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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53A GLY* 1.3 70.1 - - - -
55A PRO* 1.3 62.2 - - - +
57A SER* 2.8 8.1 + - - -
58A PHE* 2.7 32.7 + - + -
135A PRO* 3.9 7.6 - - - +
136A ASP* 2.4 29.4 + - - -
137A ARG* 3.8 27.6 - - + +
138A PHE* 3.9 27.6 - - + -
231A ARG* 3.9 5.5 + - - -
233A LEU* 3.6 18.8 - - + +
252A TYR* 5.8 1.4 - - - -
253A VAL* 5.3 0.2 - - - +
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Residues in contact with PRO 55 (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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12A TYR* 3.3 30.3 - - + +
14A ASN* 4.3 11.7 - - - +
53A GLY* 3.4 1.3 - - - -
54A THR* 1.3 92.5 - - - +
56A ILE* 1.3 57.8 + - - +
58A PHE* 2.7 31.0 + - + +
59A ARG* 2.8 13.3 + - - +
137A ARG* 3.7 33.8 - - + +
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Residues in contact with ILE 56 (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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12A TYR* 3.3 34.8 + - + +
13A ALA 3.9 14.1 - - - +
14A ASN* 3.9 10.1 + - + -
50A ASP 3.9 3.4 - - - +
51A GLU* 3.4 38.1 - - - +
52A HIS 3.6 0.9 - - - +
53A GLY 4.2 3.8 - - - +
54A THR 3.5 0.2 - - - -
55A PRO* 1.3 75.1 - - - +
57A SER* 1.3 61.4 + - - +
59A ARG* 3.5 3.5 + - - +
60A ALA* 3.1 21.1 + - - +
67A PRO* 3.9 16.6 - - + +
70A ILE* 3.7 19.5 - - + +
71A VAL* 3.7 19.5 - - + -
235A TRP* 4.2 4.9 - - - +
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Residues in contact with SER 57 (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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53A GLY 3.1 13.1 + - - -
54A THR* 2.8 16.2 + - - -
56A ILE* 1.3 76.2 - - - +
58A PHE* 1.3 66.2 + - - +
60A ALA* 3.0 20.7 + - - +
61A LEU* 3.3 5.9 + - - +
67A PRO* 4.3 7.6 - - - -
138A PHE* 5.1 7.7 - - - -
233A LEU* 4.0 18.4 - - - +
235A TRP* 3.7 23.9 - - - +
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Residues in contact with PHE 58 (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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54A THR* 2.7 13.2 + - + +
55A PRO* 2.7 15.5 + - + +
57A SER* 1.3 69.5 - - - +
59A ARG* 1.3 66.6 + - - +
61A LEU* 2.8 22.9 + - + +
62A LYS* 3.0 30.3 + - + -
137A ARG* 3.4 44.9 - - + +
138A PHE* 4.6 23.0 - + + -
152A LYS* 3.3 37.5 - - + -
174A ALA* 5.2 14.4 - - + -
175A ILE* 6.5 0.2 - - + -
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Residues in contact with ARG 59 (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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14A ASN* 2.8 47.7 + - - +
15A GLY* 5.3 0.4 - - - -
55A PRO 2.8 9.3 + - - +
56A ILE 3.6 6.3 - - - +
58A PHE* 1.3 75.6 - - - +
60A ALA* 1.3 55.6 + - - +
62A LYS* 3.1 28.3 - - + +
63A GLU* 2.9 35.0 + - + +
65A ARG* 4.5 13.9 - - - +
70A ILE* 3.2 33.1 - - + +
74A PHE* 3.8 23.6 - - - -
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Residues in contact with ALA 60 (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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56A ILE 3.1 8.4 + - - +
57A SER 3.0 14.5 + - - +
58A PHE 2.8 2.2 + - - -
59A ARG* 1.3 74.7 - - - +
61A LEU* 1.3 58.7 + - - +
64A GLY* 2.9 9.2 + - - -
65A ARG* 2.8 48.4 + - - +
66A SER 4.1 0.2 - - - -
67A PRO* 3.6 30.1 - - + -
70A ILE* 4.9 6.0 - - + +
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Residues in contact with LEU 61 (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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57A SER 3.3 4.1 + - - +
58A PHE* 2.8 18.4 + - + +
60A ALA* 1.3 75.5 - - - +
62A LYS* 1.3 69.8 + - - +
64A GLY* 3.2 11.8 + - - -
138A PHE* 5.4 3.4 - - + -
175A ILE* 3.7 57.9 - - + +
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Residues in contact with LYS 62 (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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58A PHE* 3.0 24.8 + - + +
59A ARG* 3.1 36.4 - - + +
61A LEU* 1.3 85.7 - - - +
63A GLU* 1.3 69.8 + - + +
64A GLY 3.4 1.6 + - - -
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Residues in contact with GLU 63 (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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59A ARG* 2.9 20.7 + - + +
62A LYS* 1.3 87.8 - - + +
64A GLY* 1.3 65.9 + - - +
65A ARG* 3.3 36.1 + - + +
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Residues in contact with GLY 64 (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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60A ALA 2.9 11.3 + - - -
61A LEU* 3.2 12.5 + - - -
62A LYS 3.2 1.0 + - - -
63A GLU* 1.3 80.0 - - - +
65A ARG* 1.3 58.7 + - - +
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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