Contacts of the helix formed by residues 42 - 56 (chain A) in PDB entry 3D77
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 GLU 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLN* 4.6 4.9 - - - +
40A VAL* 2.9 30.0 + - + +
41A ASN* 1.3 73.9 - - - +
43A PRO* 1.4 73.8 - - - +
44A SER* 3.1 4.9 - - - +
45A ILE* 2.9 16.5 + - + +
46A THR* 2.9 19.9 + - - +
120A NA 2.8 26.9 - - - -
124A EDO 4.3 16.9 + - - -
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Residues in contact with PRO 43 (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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24A HIS* 4.6 0.6 - - - +
41A ASN* 3.8 3.8 - - - +
42A GLU* 1.4 84.7 - - - +
44A SER* 1.3 58.1 + - - +
46A THR* 3.3 11.9 - - - +
47A CYS* 2.8 41.8 + - - +
98A CYS* 5.8 0.9 - - + -
120A NA 3.7 9.4 - - - -
122A EDO 3.7 24.5 - - - +
123A EDO 3.9 18.6 - - - +
124A EDO 3.6 30.7 - - - +
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Residues in contact with SER 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A HIS* 3.2 25.4 - - - +
25A GLY* 3.9 16.6 - - - -
26A THR* 2.7 29.3 + - - -
30A GLN* 2.9 26.7 + - - -
42A GLU* 4.3 0.9 - - - +
43A PRO* 1.3 76.3 - - - +
45A ILE* 1.3 55.7 + - - +
48A TYR* 3.6 4.3 - - - +
120A NA 2.7 23.6 - - - -
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A THR* 3.9 20.2 - - + -
30A GLN* 4.0 36.3 - - + +
31A ILE* 4.2 6.3 - - + +
34A VAL* 3.6 25.6 - - + -
39A LEU* 3.7 20.2 - - + -
40A VAL* 3.8 9.9 - - + +
42A GLU* 2.9 23.6 + - + +
44A SER* 1.3 79.3 + - - +
46A THR* 1.3 65.3 + - - +
47A CYS 3.4 1.3 - - - -
48A TYR* 3.3 15.2 + - + +
49A MET* 3.1 26.1 + - + +
118A VAL* 5.2 1.3 - - + -
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Residues in contact with THR 46 (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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40A VAL 3.7 18.2 - - - +
41A ASN* 4.1 5.8 + - - +
42A GLU 2.9 13.7 + - - +
43A PRO* 3.3 17.8 - - - +
45A ILE* 1.3 79.3 - - + +
47A CYS* 1.3 64.3 + - - +
49A MET* 3.3 16.2 + - + +
50A TYR* 3.2 20.4 + - - +
98A CYS* 3.4 32.2 - - - +
101A ILE* 4.5 1.6 - - - +
102A TYR* 3.6 28.9 - - + -
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Residues in contact with CYS 47 (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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24A HIS* 3.5 30.6 + - + +
43A PRO* 2.8 37.3 + - - +
46A THR* 1.3 72.9 + - - +
48A TYR* 1.3 60.4 + - - +
50A TYR* 3.5 3.9 + - - +
51A CYS* 2.8 28.9 + - - +
98A CYS* 2.1 49.1 - - - -
122A EDO 4.0 11.9 - - - -
123A EDO 5.4 1.1 - - - -
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Residues in contact with TYR 48 (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 LYS* 3.3 26.6 - - - +
20A CYS* 3.6 26.5 - - + -
21A MET* 3.4 25.1 - - + -
24A HIS* 4.2 5.4 - - - -
26A THR* 3.3 30.5 - - + +
31A ILE* 3.6 15.3 - - + +
44A SER 3.6 6.0 + - - +
45A ILE* 3.3 20.5 + - + +
46A THR 3.2 0.6 - - - -
47A CYS* 1.3 76.9 - - - +
49A MET* 1.3 63.9 + - - +
51A CYS* 3.1 6.0 + - - +
52A LEU* 3.0 34.6 + - + +
118A VAL* 3.7 18.2 - - + -
119A ILE 2.6 29.7 + - - -
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Residues in contact with MET 49 (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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34A VAL* 4.3 11.2 - - - -
39A LEU* 3.8 30.7 - - + -
45A ILE* 3.1 12.2 + - + +
46A THR* 3.3 25.3 + - + +
48A TYR* 1.3 79.7 - - + +
50A TYR* 1.3 62.0 + - - +
52A LEU* 3.4 4.1 + - - +
53A LEU* 3.0 28.2 + - + +
101A ILE* 3.6 22.4 - - + +
102A TYR* 4.6 0.4 - - - -
105A ALA* 4.2 6.7 - - + -
116A TRP* 3.6 31.4 - - + -
118A VAL* 3.7 28.0 - - + -
121A NBB 5.0 2.6 + - - -
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Residues in contact with TYR 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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46A THR 3.2 12.8 + - - +
47A CYS* 3.9 9.2 - - - +
49A MET* 1.3 75.7 - - - +
51A CYS* 1.3 62.9 + - - +
53A LEU* 3.3 2.6 + - - +
54A GLU* 2.9 45.0 + - + +
59A VAL* 3.4 24.9 - - + -
60A ASP 2.9 26.0 + - - -
61A ASP* 3.7 5.0 - - - -
63A ALA* 3.8 20.9 - - + -
97A ASN* 3.6 43.2 + - + +
98A CYS* 4.5 4.0 - - - -
101A ILE* 3.8 20.9 - - + +
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Residues in contact with CYS 51 (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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19A ARG* 3.5 19.8 + - - -
20A CYS* 2.1 52.7 - - + -
23A GLU* 3.6 10.8 - - - -
24A HIS* 3.8 9.0 - - + +
47A CYS 2.8 19.7 + - - +
48A TYR 3.3 4.3 - - - +
50A TYR* 1.3 84.0 - - + +
52A LEU* 1.3 56.6 + - - +
54A GLU* 3.4 6.8 + - - +
55A ALA* 3.0 26.0 + - - +
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Residues in contact with LEU 52 (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 VAL* 4.0 3.4 - - + -
16A ASP* 4.0 13.0 - - + +
17A LYS* 3.9 32.8 - - - +
20A CYS* 3.8 4.0 - - - -
48A TYR* 3.0 24.4 + - + +
49A MET* 4.1 3.8 - - - +
51A CYS* 1.3 73.6 - - - +
53A LEU* 1.3 66.2 + - - +
55A ALA* 3.1 4.6 + - - +
56A PHE* 3.1 58.9 + - + -
118A VAL* 5.3 1.3 - - + -
119A ILE* 3.6 28.0 - - + +
121A NBB 3.6 26.2 - - - +
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Residues in contact with LEU 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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49A MET* 3.0 21.0 + - + +
50A TYR 3.7 1.1 - - - +
52A LEU* 1.3 76.0 - - - +
54A GLU* 1.3 62.0 + - - +
56A PHE* 3.2 7.5 + - - +
58A LEU* 2.9 50.6 + - + +
59A VAL* 3.7 21.8 - - + -
70A MET* 4.0 11.2 - - + -
101A ILE* 3.8 40.4 - - + -
104A LEU* 5.3 1.1 - - + -
116A TRP* 4.3 12.3 - - + -
121A NBB 3.6 36.8 - - + +
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Residues in contact with GLU 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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19A ARG* 4.9 6.4 + - - -
50A TYR* 2.9 40.5 + - + +
51A CYS* 3.6 6.8 - - - +
53A LEU* 1.3 75.4 - - - +
55A ALA* 1.3 69.5 + - - +
57A SER* 3.0 15.1 + - - -
59A VAL* 3.4 22.9 - - + +
60A ASP 5.4 1.8 - - - +
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Residues in contact with ALA 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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16A ASP* 3.6 41.1 - - + +
19A ARG* 4.0 6.5 - - - +
51A CYS 3.0 14.4 + - - +
52A LEU* 3.1 12.3 + - + +
54A GLU* 1.3 83.6 + - - +
56A PHE* 1.3 62.9 + - + +
57A SER* 3.3 4.7 + - - -
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Residues in contact with PHE 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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13A VAL* 3.2 44.9 - - + -
16A ASP* 4.9 4.7 - - + -
52A LEU* 3.1 48.6 + - + +
53A LEU 3.2 3.6 + - - +
54A GLU 3.2 0.2 - - - -
55A ALA* 1.3 84.1 - - + +
57A SER* 1.3 71.2 + - - +
58A LEU* 3.3 20.3 + - + +
69A ILE* 4.4 4.5 - - - +
73A LEU* 4.8 9.2 - - + +
119A ILE* 4.4 5.8 - - + -
121A NBB 3.6 40.8 - + - -
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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