Contacts of the helix formed by residues 40 - 56 (chain A) in PDB entry 6JGW
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 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 5.1 4.3 - - - -
38A LEU 4.6 3.8 - - - +
39A TYR* 1.3 80.6 - - - +
41A GLN* 1.3 64.2 + - - +
42A ALA* 3.0 22.1 + - - +
43A HIS* 3.0 38.9 + - + +
44A VAL* 3.1 15.7 + - - +
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Residues in contact with GLN 41 (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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1A MET* 5.6 0.6 - - - +
40A THR* 1.3 74.6 - - - +
42A ALA* 1.3 63.0 + - - +
44A VAL* 3.1 26.6 + - - +
45A GLU* 3.1 48.7 + - - +
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Residues in contact with ALA 42 (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 THR* 3.0 11.9 + - - +
41A GLN* 1.3 78.9 - - - +
43A HIS* 1.3 63.0 + - + +
45A GLU* 3.2 14.2 + - - +
46A ARG* 2.9 28.7 + - - +
70A ARG* 4.6 2.4 + - - -
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Residues in contact with HIS 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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6A LEU* 4.6 5.1 - - + +
26A LEU* 4.7 7.7 - - + +
27A PRO* 3.7 32.7 - - + +
29A PRO* 4.0 25.8 - - + -
30A ALA 5.6 0.2 - - - -
38A LEU 4.7 0.4 - - - -
39A TYR* 3.5 27.0 - + + -
40A THR* 3.0 42.2 + - + +
42A ALA* 1.3 77.6 - - + +
44A VAL* 1.3 66.4 + - - +
46A ARG* 3.6 9.1 - - - +
47A LEU* 2.8 26.7 + - - +
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.2 16.2 - - + -
6A LEU* 3.9 21.5 - - + -
9A ALA* 4.4 14.4 - - + -
10A THR* 3.9 11.5 - - + +
40A THR 3.1 14.2 + - - +
41A GLN* 3.1 32.1 + - - +
43A HIS* 1.3 78.1 - - - +
45A GLU* 1.3 59.3 + - + +
47A LEU* 3.8 1.0 - - - +
48A THR* 2.8 42.4 + - - +
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Residues in contact with GLU 45 (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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41A GLN* 3.1 41.8 + - - +
42A ALA* 3.6 12.6 - - - +
44A VAL* 1.3 79.6 - - + +
46A ARG* 1.3 58.3 + - - +
48A THR* 3.3 7.8 + - - -
49A PHE* 2.9 29.3 + - - +
70A ARG* 4.0 16.2 + - - +
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Residues in contact with ARG 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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24A GLN 5.8 0.6 + - - -
25A LEU 3.0 26.0 + - - -
26A LEU* 3.9 7.2 - - + -
27A PRO* 3.7 25.6 - - - +
42A ALA 2.9 16.8 + - - +
43A HIS* 3.6 11.2 - - - +
45A GLU* 1.3 76.7 - - - +
47A LEU* 1.3 57.9 + - - +
49A PHE* 3.3 3.7 + - - +
50A ILE* 2.9 39.8 + - + +
67A LEU* 3.9 26.8 - - + +
70A ARG* 3.5 29.7 - - - +
71A ASP* 2.9 40.8 + - - -
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Residues in contact with LEU 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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6A LEU* 4.1 13.5 - - + -
10A THR* 3.6 30.5 - - + +
12A CYS* 4.7 3.1 - - - -
17A ILE* 3.9 27.1 - - + -
20A TYR* 3.9 33.9 - - + -
26A LEU* 4.5 12.8 - - + +
43A HIS 2.8 18.3 + - - +
44A VAL* 3.8 2.7 - - - +
46A ARG* 1.3 74.6 - - - +
48A THR* 1.3 61.4 + - - +
50A ILE* 3.1 11.4 + - + -
51A ARG* 2.8 38.2 + - + +
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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
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10A THR* 3.7 17.3 - - - +
44A VAL* 2.8 29.7 + - - +
45A GLU* 3.5 7.8 - - - -
47A LEU* 1.3 78.0 - - - +
49A PHE* 1.3 62.0 + - - +
51A ARG* 3.3 5.6 + - - +
52A ASN* 3.0 37.9 + - - +
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Residues in contact with PHE 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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45A GLU 2.9 13.3 + - - +
46A ARG* 3.5 7.6 - - - +
47A LEU 3.2 0.2 - - - -
48A THR* 1.3 77.0 - - - +
50A ILE* 1.3 65.6 + - + +
52A ASN* 3.2 9.5 + - - +
53A CYS* 3.0 39.8 + - - -
63A ILE* 5.2 2.2 - - + -
66A LEU* 4.0 28.9 - - + -
67A LEU* 4.1 28.7 - - + -
70A ARG* 4.3 24.5 - - + +
101B LEU* 3.6 25.6 - - + -
104B GLN* 4.0 29.4 - - + -
105B LEU* 4.5 7.2 - - + -
108B LEU* 5.1 7.4 - - + -
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Residues in contact with ILE 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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20A TYR* 3.7 34.3 - - + +
25A LEU* 4.1 32.3 - - + +
26A LEU* 3.9 22.9 - - + -
46A ARG* 2.9 33.0 + - + +
47A LEU* 3.4 9.2 - - + +
49A PHE* 1.3 78.8 - - + +
51A ARG* 1.3 64.8 + - - +
53A CYS* 3.1 9.8 + - - +
54A ARG* 3.0 24.1 + - + +
63A ILE* 4.1 9.6 - - + +
67A LEU* 4.2 19.5 - - + -
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Residues in contact with ARG 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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10A THR 4.7 8.5 - - - +
11A ASP 4.9 6.1 + - - -
12A CYS* 3.7 30.9 - - + +
16A THR* 4.2 9.3 + - - +
20A TYR* 2.5 34.4 + - - -
47A LEU* 2.8 33.4 + - + +
48A THR* 3.8 5.8 - - - +
49A PHE 3.2 0.2 - - - -
50A ILE* 1.3 77.3 - - - +
52A ASN* 1.3 65.3 + - - +
54A ARG* 3.0 17.4 + - - +
55A THR* 3.0 26.0 + - + +
16C C 3.0 26.5 + - - -
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Residues in contact with ASN 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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48A THR* 3.0 32.8 + - - +
49A PHE* 3.6 9.3 - - - +
51A ARG* 1.3 77.0 - - - +
53A CYS* 1.3 64.0 + - - +
55A THR* 2.6 31.9 + - - +
56A LEU 3.2 3.3 + - - -
97B GLY* 3.3 35.8 + - - +
100B ALA* 4.1 13.9 - - - +
101B LEU* 3.8 23.6 - - + +
104B GLN* 6.3 1.2 - - - +
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Residues in contact with CYS 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 PHE* 3.0 49.6 + - - -
50A ILE* 3.4 8.1 - - - +
52A ASN* 1.3 73.6 - - - +
54A ARG* 1.3 59.9 + - - +
56A LEU* 3.0 23.0 + - - +
58A MET* 3.2 42.8 + - + +
63A ILE* 3.7 19.7 - - + -
66A LEU* 4.3 2.0 - - - -
101B LEU* 3.8 16.1 - - - +
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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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20A TYR* 3.8 9.9 - - - +
50A ILE* 3.0 16.9 + - + +
51A ARG* 3.0 22.0 + - - +
53A CYS* 1.3 74.5 - - - +
55A THR* 1.3 60.1 + - - +
57A ASP* 3.0 44.0 + - - +
58A MET 2.5 36.9 + - - -
59A THR* 4.4 1.4 - - - +
60A LEU* 4.2 8.7 - - - -
63A ILE* 3.7 14.1 - - + -
94A ARG* 4.9 0.5 + - - -
94B ARG* 4.8 1.9 + - - -
15C G 3.5 37.2 + - - -
16C C 3.0 27.0 + - - +
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Residues in contact with THR 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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51A ARG* 3.0 18.4 + - + +
52A ASN* 2.6 28.0 + - - +
54A ARG* 1.3 75.2 - - + +
56A LEU* 1.3 56.4 + - - +
57A ASP 3.2 0.9 - - - -
94A ARG* 2.9 25.0 + - - +
94B ARG* 3.4 49.0 + - + +
97B GLY* 5.1 1.5 - - - -
98B LEU* 3.4 22.0 + - - +
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Residues in contact with LEU 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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52A ASN 3.2 5.7 + - - +
53A CYS* 3.0 13.0 + - - +
55A THR* 1.3 76.9 + - - +
57A ASP* 1.3 66.5 + - - +
58A MET* 3.2 30.9 + - + +
87A HIS* 4.3 12.3 - - + +
90A HIS* 3.9 16.2 - - + +
91A VAL* 3.8 46.2 - - + +
94A ARG* 3.9 25.1 + - + +
98B LEU* 4.2 9.6 - - + -
101B LEU* 4.3 2.7 - - + -
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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