Contacts of the helix formed by residues 61 - 74 (chain A) in PDB entry 2RFQ
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 ASP 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A HIS* 3.8 23.4 + - - +
59A GLN 4.0 0.2 + - - -
60A ALA* 1.3 73.5 - - - +
62A PRO* 1.3 74.2 - - - +
63A VAL* 3.0 24.7 + - - +
64A LEU* 3.0 24.7 + - + +
65A PHE 3.5 2.9 + - - -
302A TYR* 3.7 31.8 + - + +
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Residues in contact with PRO 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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50A LEU* 4.4 12.1 - - + -
60A ALA 3.2 7.1 - - - +
61A ASP* 1.3 89.1 - - - +
63A VAL* 1.3 61.3 + - - +
65A PHE* 3.1 4.2 + - + +
66A TYR* 3.0 39.4 + - + -
225A VAL* 3.8 14.4 - - + -
228A MSE 4.1 9.4 - - + -
233A ILE* 4.5 9.2 - - + -
298A VAL* 3.7 22.7 - - + -
302A TYR* 3.4 34.5 - - + -
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Residues in contact with VAL 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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4A HIS* 3.8 19.7 - - + +
61A ASP* 3.0 15.5 + - - +
62A PRO* 1.3 77.5 - - + +
64A LEU* 1.3 58.4 + - - +
66A TYR* 3.8 5.0 - - - +
67A SER* 2.7 43.0 + - - +
291A TRP* 4.9 1.3 - - + -
295A SER* 3.7 39.9 - - - +
298A VAL* 3.7 16.8 - - + -
299A ALA* 3.8 17.5 - - + +
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Residues in contact with LEU 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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4A HIS* 3.8 37.3 - - + +
7A HIS* 3.4 39.5 - - + +
9A VAL* 5.7 0.4 - - + -
10A MSE 3.7 30.7 - - + -
49A LEU* 3.7 24.9 - - + -
60A ALA* 4.0 12.3 - - + -
61A ASP* 3.0 14.7 + - + +
63A VAL* 1.3 79.7 - - - +
65A PHE* 1.3 62.5 + - - +
67A SER* 3.3 2.2 + - - -
68A ALA* 3.0 20.4 + - - +
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Residues in contact with PHE 65 (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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46A PHE* 3.6 26.7 - + - -
49A LEU* 4.0 23.6 - - + -
50A LEU* 3.6 44.2 - - + -
60A ALA* 5.2 0.8 - - + +
61A ASP 3.5 2.4 + - - +
62A PRO 3.1 8.4 + - - +
64A LEU* 1.3 79.2 - - - +
66A TYR* 1.3 75.6 + + - +
68A ALA* 3.1 6.4 + - - +
69A VAL* 3.0 42.1 + - + +
84A SER 3.5 20.4 - - - -
87A GLY* 3.8 16.4 - - - -
88A VAL* 3.7 11.0 - - + -
237A THR* 3.5 21.5 - - - -
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Residues in contact with TYR 66 (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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62A PRO* 3.0 36.9 + - + +
63A VAL* 4.2 4.3 - - - +
65A PHE* 1.3 92.0 - + - +
67A SER* 1.3 56.2 + - - +
69A VAL* 3.3 5.9 + - + +
70A ARG* 2.9 29.8 + - - +
88A VAL* 4.8 0.7 - - - +
233A ILE* 2.7 45.2 + - + +
236A THR* 3.6 26.5 - - + -
237A THR* 3.6 33.4 + - - -
240A ALA* 4.0 17.6 - - + +
291A TRP* 3.6 16.2 - - + -
294A LEU* 5.9 0.2 - - + -
295A SER* 6.1 3.6 - - - -
298A VAL* 3.9 24.2 - - + -
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Residues in contact with SER 67 (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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4A HIS* 4.3 9.3 + - - +
10A MSE 3.9 23.4 - - - +
63A VAL* 2.7 30.8 + - - +
64A LEU* 3.5 7.4 - - - -
66A TYR* 1.3 77.3 - - - +
68A ALA* 1.3 62.0 + - - +
70A ARG* 3.4 10.1 + - - +
71A LYS* 3.1 22.9 + - - +
291A TRP* 3.4 24.0 - - - -
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Residues in contact with ALA 68 (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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9A VAL* 5.1 0.7 - - + -
10A MSE 3.6 14.9 - - - -
13A LEU* 3.7 21.9 - - + +
46A PHE* 3.8 15.0 - - + -
49A LEU* 3.8 10.5 - - + -
64A LEU 3.0 12.7 + - - +
65A PHE 3.1 9.2 + - - +
67A SER* 1.3 74.5 - - - +
69A VAL* 1.3 65.4 + - - +
71A LYS* 3.2 4.2 + - - +
72A ILE* 3.0 29.6 + - - +
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Residues in contact with VAL 69 (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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46A PHE* 3.9 11.4 - - + -
65A PHE* 3.0 30.5 + - + +
66A TYR* 3.5 11.4 - - + +
68A ALA* 1.3 72.8 - - - +
70A ARG* 1.3 65.1 - - - +
72A ILE* 3.2 8.2 + - - +
73A ALA* 2.9 23.6 + - - +
80A GLY* 4.1 3.9 - - - +
84A SER* 3.6 47.1 - - - +
240A ALA* 3.9 4.3 - - + -
241A PRO* 3.7 28.9 - - + -
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Residues in contact with ARG 70 (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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5A ASP* 5.9 0.6 + - - -
10A MSE 6.0 3.6 - - - +
66A TYR 2.9 17.8 + - - +
67A SER* 3.5 10.0 + - - +
69A VAL* 1.3 75.9 - - - +
71A LYS* 1.3 63.7 + - - +
74A SER* 3.1 21.0 + - - -
240A ALA 4.2 6.7 - - - +
243A VAL* 4.7 0.2 - - - -
244A GLY* 3.4 30.1 - - - +
247A TYR* 3.2 51.9 + - + -
291A TRP* 3.3 50.3 - - + +
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Residues in contact with LYS 71 (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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5A ASP* 2.8 28.7 + - - -
10A MSE 3.6 29.8 - - - +
13A LEU* 3.7 27.4 - - + -
14A ASP* 2.7 30.8 + - - +
17A LEU* 3.6 23.2 - - + +
67A SER 3.1 11.4 + - - +
68A ALA 3.4 7.6 - - - +
70A ARG* 1.3 79.1 - - - +
72A ILE* 1.3 63.2 + - - +
74A SER* 2.6 25.5 + - - +
75A ALA 3.6 2.1 + - - -
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Residues in contact with ILE 72 (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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13A LEU* 4.0 20.2 - - + -
17A LEU* 4.3 7.9 - - + -
20A LEU* 4.0 11.3 - - + +
41A LEU* 3.8 16.8 - - + -
46A PHE* 3.9 23.6 - - + -
68A ALA 3.0 22.2 + - - +
69A VAL* 3.8 3.8 - - - +
71A LYS* 1.3 75.2 - - + +
73A ALA* 1.3 58.4 + - - +
75A ALA* 3.0 21.3 + - - +
76A CYS 3.2 10.2 + - - +
79A THR* 3.8 20.2 - - + -
80A GLY* 3.7 22.2 - - - +
83A SER* 3.8 22.2 - - - +
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Residues in contact with ALA 73 (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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69A VAL 2.9 17.3 + - - +
70A ARG 3.9 3.8 - - - +
72A ILE* 1.3 77.4 - - - +
74A SER* 1.3 60.1 + - - +
75A ALA 3.1 0.9 + - - -
76A CYS 3.6 16.5 + - - +
77A GLY 3.7 1.8 + - - +
80A GLY* 3.7 11.2 - - - -
241A PRO* 3.2 38.1 - - + +
244A GLY* 3.9 2.2 - - - -
245A MSE 3.7 10.6 - - + +
355A PHE* 3.6 15.9 - - - -
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Residues in contact with SER 74 (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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17A LEU* 4.4 8.1 - - - +
21A ARG* 4.7 9.3 + - - -
70A ARG 3.1 11.7 + - - -
71A LYS* 2.6 23.1 + - - -
73A ALA* 1.3 76.7 - - - +
75A ALA* 1.3 56.4 + - - +
244A GLY 3.1 20.6 + - - -
247A TYR* 4.3 7.9 - - - -
248A GLY* 3.2 28.0 - - - -
251A ASP* 5.7 2.0 - - - -
355A PHE* 3.3 8.6 - - - -
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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