Contacts of the helix formed by residues 47 - 60 (chain A) in PDB entry 3A9L
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 47 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLY 4.5 2.8 + - - -
45A GLU 3.4 0.2 + - - -
46A VAL* 1.3 77.4 - - - +
48A THR* 1.3 63.5 + - - +
49A THR 3.3 2.4 - - - +
50A GLU* 3.2 19.8 + - - +
51A LEU* 3.1 26.2 + - - +
171A ARG* 5.0 1.8 - - - -
174A PHE* 4.5 13.4 - - - -
175A PHE* 3.9 17.7 - - - -
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Residues in contact with THR 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A SER* 3.8 15.9 - - - +
40A HIS 3.3 0.3 + - - -
41A ALA* 3.3 18.4 - - - -
45A GLU* 2.7 27.8 + - + +
46A VAL 3.5 0.6 + - - -
47A GLY* 1.3 72.9 + - - +
49A THR* 1.3 66.7 + - - +
51A LEU* 4.1 4.6 - - - +
52A ILE* 2.9 31.5 + - - +
65A LEU* 4.9 0.2 - - - -
102A PHE* 3.2 37.0 - - + +
103A HIS* 3.9 15.9 - - - +
104A GLY* 5.1 0.7 - - - -
166A ILE* 5.8 3.1 - - + -
171A ARG* 5.2 4.2 - - - +
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Residues in contact with THR 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ALA* 3.4 4.7 - - - +
42A GLY* 2.8 25.0 + - - +
47A GLY 3.3 1.0 - - - +
48A THR* 1.3 80.3 + - - +
50A GLU* 1.3 77.9 + - + +
52A ILE* 3.3 1.4 + - - +
53A TYR* 2.9 59.7 + - + +
65A LEU* 3.9 10.3 - - + +
67A GLN* 2.6 30.3 + - - +
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Residues in contact with GLU 50 (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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42A GLY* 5.7 0.9 - - - +
47A GLY* 3.2 28.8 + - - +
48A THR 3.3 0.4 - - - -
49A THR* 1.3 93.6 - - + +
51A LEU* 1.3 67.1 + - - +
53A TYR* 3.4 7.9 + - - +
54A ARG* 3.2 14.6 + - - +
175A PHE* 3.8 12.1 - - + -
182A LYS* 5.3 6.4 + - - -
185A ARG* 3.7 48.5 + - + +
188A VAL* 5.2 2.2 - - + -
192A PHE* 3.1 25.0 - - + -
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Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLY 3.1 18.8 + - - +
48A THR* 4.1 3.4 - - - +
50A GLU* 1.3 79.1 - - - +
52A ILE* 1.3 61.7 + - - +
54A ARG* 3.4 1.0 + - - +
55A VAL* 3.0 26.2 + - + +
102A PHE* 3.4 36.8 - - + -
166A ILE* 3.7 22.7 - - + -
174A PHE* 4.3 7.6 - - + -
192A PHE* 3.4 18.5 - - + -
195A TYR* 3.8 19.5 - - + -
196A ALA* 3.6 36.8 - - + +
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Residues in contact with ILE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 3.9 16.8 - - + +
37A PHE 3.4 33.4 - - - +
38A SER* 3.5 14.1 - - - +
48A THR 2.9 22.4 + - - +
49A THR 3.8 2.7 - - - +
51A LEU* 1.3 77.3 - - - +
53A TYR* 1.3 57.6 + - - +
55A VAL* 3.3 5.1 + - - +
56A VAL* 2.9 33.5 + - + +
63A LEU* 3.9 18.2 - - + -
65A LEU* 3.5 21.3 - - + -
102A PHE* 3.3 30.7 - - + -
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Residues in contact with TYR 53 (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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26A GLU* 2.5 29.5 + - - -
49A THR* 2.9 37.8 + - + +
50A GLU* 3.5 12.1 - - - +
52A ILE* 1.3 77.6 - - - +
54A ARG* 1.3 52.9 + - - +
56A VAL* 3.4 5.3 + - - +
57A GLU* 2.8 55.6 + - - +
63A LEU* 3.9 18.2 - - + -
65A LEU* 3.3 26.6 - - + +
67A GLN* 5.1 1.0 + - - -
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Residues in contact with ARG 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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50A GLU 3.2 2.5 + - - +
51A LEU 3.8 2.2 - - - +
53A TYR* 1.3 76.3 - - - +
55A VAL* 1.3 61.1 + - - +
57A GLU* 3.7 23.3 + - - +
58A LEU* 2.8 63.0 + - + +
192A PHE* 3.5 36.8 - - + -
193A LEU* 3.8 26.8 + - + +
196A ALA* 3.4 22.0 - - + +
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Residues in contact with VAL 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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36A TYR* 3.6 43.3 - - + -
51A LEU* 3.0 39.4 + - + +
52A ILE* 3.9 5.8 - - - +
54A ARG* 1.3 76.2 - - - +
56A VAL* 1.3 52.4 + - - +
58A LEU* 3.5 5.5 + - - -
59A THR* 2.5 43.1 + - + +
102A PHE* 4.2 9.9 - - + -
196A ALA* 4.0 18.8 - - + +
199A ILE* 3.8 19.1 - - + -
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Residues in contact with VAL 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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28A LYS* 5.6 3.6 - - + -
30A GLN* 3.6 12.4 + - - +
36A TYR* 4.1 15.0 - - + -
52A ILE* 2.9 22.2 + - + +
53A TYR 3.7 3.6 - - - +
55A VAL* 1.3 75.1 - - - +
57A GLU* 1.3 63.5 + - + +
59A THR* 3.6 4.7 - - - -
60A GLY* 2.8 29.5 + - - -
61A GLY 3.4 16.6 - - - +
62A SER 3.7 22.7 - - - +
63A LEU* 3.9 28.3 - - + -
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Residues in contact with GLU 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 TYR* 2.8 47.6 + - - +
54A ARG* 3.7 31.3 + - - +
56A VAL* 1.3 78.2 - - + +
58A LEU* 1.3 62.2 + - - +
59A THR 3.7 0.2 + - - -
60A GLY 4.5 1.4 + - - -
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Residues in contact with LEU 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 ARG* 2.8 52.8 + - + +
55A VAL 3.8 4.0 - - - +
57A GLU* 1.3 77.5 - - - +
59A THR* 1.3 58.3 + - - +
193A LEU 5.1 0.9 - - - +
196A ALA* 3.6 38.8 - - + +
197A GLU* 3.7 19.1 - - + +
200A LYS* 3.2 34.9 - - + +
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Residues in contact with THR 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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31A ASN* 5.3 2.4 + - - -
36A TYR* 3.3 15.5 - - + +
55A VAL* 2.5 26.8 + - + +
56A VAL* 3.6 0.7 - - - -
58A LEU* 1.3 79.3 - - - +
60A GLY* 1.3 62.1 + - - +
61A GLY 3.0 15.1 + - - -
200A LYS* 3.7 31.6 - - + -
203A GLU* 3.2 30.9 - - - +
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Residues in contact with GLY 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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30A GLN* 3.5 24.6 + - - +
31A ASN* 3.6 17.3 + - - +
56A VAL 2.8 18.6 + - - -
57A GLU 4.5 1.4 + - - -
58A LEU 3.9 0.6 - - - -
59A THR* 1.3 73.0 - - - +
61A GLY* 1.3 65.3 + - - +
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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