Contacts of the helix formed by residues 51 - 66 (chain A) in PDB entry 2I9W
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 THR 51 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ALA* 3.4 2.6 - - - +
50A ASP* 1.3 90.5 - - + +
52A ALA* 1.3 58.7 + - - +
53A GLU* 3.4 6.9 + - - +
54A HIS* 3.1 43.4 + - + +
55A LEU* 2.9 26.7 + - - +
105A HIS* 4.0 17.1 - - + -
107A PRO* 6.1 0.7 - - + -
150A TRP* 3.5 11.4 - - - +
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR* 1.3 69.9 - - - +
53A GLU* 1.3 59.3 + - - +
55A LEU* 3.2 6.2 + - - +
56A MSE 2.8 31.5 + - - +
105A HIS* 4.1 4.4 + - - +
114A ALA* 3.6 31.0 - - + -
116A VAL* 3.6 7.9 - - + +
137A PHE* 3.7 30.3 - - + -
150A TRP* 3.7 17.1 - - + +
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Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR* 3.3 3.6 + - - +
52A ALA* 1.3 76.9 - - - +
54A HIS* 1.3 69.9 + - + +
56A MSE 3.3 3.3 + - - +
57A ARG* 3.0 57.3 + - - +
102A VAL* 3.9 25.4 - - + +
105A HIS* 3.5 43.3 + - + +
116A VAL* 3.6 11.8 - - + +
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Residues in contact with HIS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 5.9 5.4 - + + -
49A ALA* 4.0 13.0 - - + -
50A ASP* 3.9 15.5 - - + +
51A THR* 3.1 45.9 + - + +
53A GLU* 1.3 85.4 - - - +
55A LEU* 1.3 62.7 + - - +
57A ARG* 3.3 14.3 + - - +
58A THR* 3.0 27.5 + - + +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 3.6 17.4 - - + +
51A THR 2.9 14.3 + - - +
52A ALA* 3.6 9.6 - - - +
54A HIS* 1.3 76.8 - - - +
56A MSE 1.3 57.4 + - - +
58A THR* 2.6 21.7 + - - +
59A ARG* 2.9 21.6 + - + +
70A TYR* 3.8 13.5 - - - +
74A THR* 3.7 33.4 - - + +
137A PHE* 3.8 23.1 - - + -
150A TRP* 3.3 37.5 - - + +
151A TYR* 4.0 5.2 - - - +
152A PHE 4.1 3.6 - - - +
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Residues in contact with MSE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA 2.8 19.8 + - - +
53A GLU 3.3 3.8 + - - +
55A LEU* 1.3 72.0 - - - +
57A ARG* 1.3 63.5 + - + +
59A ARG* 3.2 20.0 + - - +
60A TYR* 3.0 25.1 + - + +
63A PHE* 6.0 3.6 - - - -
100A LEU* 5.4 4.0 - - + -
102A VAL* 6.3 1.3 - - + -
116A VAL* 4.2 13.0 - - + -
118A PHE* 2.7 51.4 - - + -
135A SER* 2.6 42.8 - - - +
137A PHE* 3.7 20.4 - - + -
152A PHE* 4.3 6.5 - - + -
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Residues in contact with ARG 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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10A CYS* 3.1 50.2 + - + +
11A GLN* 4.0 11.0 - - - +
28A CYS* 6.0 1.6 - - - -
29A CYS* 4.0 4.3 - - - -
53A GLU* 3.0 45.1 + - - +
54A HIS* 3.6 16.3 + - - +
56A MSE 1.3 76.3 - - - +
58A THR* 1.3 62.4 + - + +
60A TYR* 3.3 3.8 + - - +
61A SER* 3.0 26.7 + - - -
100A LEU* 3.9 19.2 - - + +
102A VAL* 3.7 22.9 - - + +
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Residues in contact with THR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A CYS* 3.7 22.2 - - + -
32A TYR* 3.8 33.2 - - + -
33A HIS* 2.9 26.5 + - - -
49A ALA* 5.1 2.9 - - + -
54A HIS* 3.0 17.8 + - + +
55A LEU* 2.6 24.4 + - - +
57A ARG* 1.3 76.3 - - + +
59A ARG* 1.3 56.9 + - - +
61A SER 3.5 0.3 + - - -
62A ALA* 3.0 13.2 + - - +
70A TYR* 2.7 29.1 + - - +
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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
----------------------------------------------------------
55A LEU* 2.9 27.9 + - + +
56A MSE 3.6 18.8 - - - +
58A THR* 1.3 74.6 - - - +
60A TYR* 1.3 64.7 + - - +
62A ALA* 3.0 2.6 + - - -
63A PHE* 2.9 36.1 + - + -
70A TYR* 4.2 6.7 - - + -
71A ILE* 3.0 56.3 + - + +
74A THR* 2.9 36.7 + - - +
75A THR* 3.5 8.5 + - - -
137A PHE* 4.5 7.4 - - - -
152A PHE* 3.3 46.7 - - - +
154A ASP* 5.3 1.2 + - - -
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Residues in contact with TYR 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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9A PRO* 3.4 23.0 + - + +
10A CYS* 3.9 17.0 - - - -
56A MSE 3.0 15.0 + - + +
57A ARG 3.3 6.7 + - - +
59A ARG* 1.3 73.6 - - - +
61A SER* 1.3 65.3 + - - +
63A PHE* 3.0 25.0 + + - +
64A VAL* 3.0 36.6 + - + +
97A TRP* 3.8 31.2 - + - +
98A ALA 4.0 0.2 + - - -
99A GLY* 3.0 44.2 + - - -
100A LEU* 4.0 30.1 - - + -
118A PHE* 6.0 2.2 - + + -
120A ALA* 4.3 11.4 - - + -
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Residues in contact with SER 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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8A CYS* 3.8 1.4 - - - -
9A PRO* 4.0 20.6 - - - -
10A CYS 3.3 20.8 + - - -
29A CYS* 3.2 21.3 - - - -
33A HIS* 3.7 19.5 - - - -
57A ARG 3.0 16.8 + - - -
58A THR 3.8 0.4 - - - -
60A TYR* 1.3 76.0 - - - +
62A ALA* 1.3 57.6 + - - +
64A VAL* 3.4 0.5 + - - +
65A LEU* 2.9 35.3 + - - +
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A HIS* 3.7 9.1 + - - +
58A THR 3.0 14.7 + - - +
59A ARG 3.0 8.3 + - - +
61A SER* 1.3 74.4 - - - +
63A PHE* 1.3 60.7 + - - +
65A LEU 4.6 0.2 - - - +
66A VAL* 3.0 7.8 + - - -
67A LYS* 2.9 44.9 + - + +
70A TYR* 3.7 24.9 - - + -
71A ILE* 3.7 11.6 - - + +
92A ALA* 5.0 0.5 - - - +
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Residues in contact with PHE 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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56A MSE 6.0 3.4 - - - -
59A ARG* 2.9 38.2 + - + -
60A TYR* 3.0 18.1 + + + +
62A ALA* 1.3 74.9 - - - +
64A VAL* 1.3 64.3 + - - +
66A VAL* 3.2 9.2 + - - -
71A ILE* 3.5 41.3 - - + -
88A ILE* 4.4 6.3 - - + -
91A TRP* 3.7 36.6 - + - -
92A ALA* 3.4 29.9 - - + +
97A TRP* 3.9 27.4 - + + +
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Residues in contact with VAL 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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3A PHE* 6.4 1.6 - - + -
9A PRO* 3.8 27.1 - - + -
60A TYR* 3.0 49.8 + - + +
61A SER 3.4 2.2 + - - +
63A PHE* 1.3 78.8 - - - +
65A LEU* 1.3 65.7 + - + +
66A VAL* 3.3 7.2 + - - +
92A ALA 5.0 0.7 - - - +
97A TRP* 3.7 30.9 - - + +
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Residues in contact with LEU 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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3A PHE* 3.8 42.4 - - + -
9A PRO* 3.9 22.0 - - + -
25A TYR* 3.3 52.3 - - + +
33A HIS* 4.5 1.8 - - + -
61A SER 2.9 20.2 + - - +
64A VAL* 1.3 79.9 - - + +
66A VAL* 1.3 70.7 + - - +
67A LYS* 3.6 21.4 - - + +
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Residues in contact with VAL 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 ALA 3.0 7.7 + - - -
63A PHE 3.2 11.3 + - - +
64A VAL 4.0 6.7 - - - +
65A LEU* 1.3 81.6 - - - +
67A LYS* 1.3 60.7 + - - +
68A PRO* 3.3 9.8 - - + +
69A GLU* 4.8 0.5 - - - +
89A GLU* 3.9 41.7 - - + +
92A ALA* 4.4 4.5 - - + +
93A LYS* 3.9 35.9 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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