Contacts of the helix formed by residues 39 - 51 (chain A) in PDB entry 5H4G
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 ILE 39 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU 3.6 1.0 + - - -
38A SER* 1.3 74.0 - - - +
40A VAL* 1.3 66.2 + - + +
42A VAL* 3.8 4.7 - - + -
43A TYR* 2.9 27.0 + - - +
60A PHE* 4.1 25.4 - - + -
69A ILE* 3.8 25.1 - - + +
70A VAL 2.9 21.9 + - - +
71A PRO* 3.9 4.9 - - + -
72A LEU* 3.8 20.0 - - + +
201A ZN 4.1 7.2 - - - -
72B LEU* 3.6 39.7 - - + +
73B LEU 5.4 0.2 - - - +
74B ASP* 5.0 3.4 - - - +
77B ALA* 4.1 11.9 - - + -
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A SER* 3.0 8.8 + - - +
39A ILE* 1.3 85.1 - - + +
41A THR* 1.3 61.4 + - - +
43A TYR* 3.6 7.4 - - + -
44A ARG* 3.0 23.0 + - - +
72A LEU* 4.5 10.5 - - + -
96A MET* 4.8 1.3 - - + -
97A GLU* 4.0 17.0 - - + -
100A ILE* 3.9 24.9 - - + -
101A THR* 5.3 2.0 - - - +
72B LEU* 4.0 19.5 - - + -
96B MET* 3.0 47.6 - - + -
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Residues in contact with THR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE 3.4 26.4 + - - +
10A ASP* 3.6 4.1 - - - +
11A SER* 3.5 21.6 + - - +
14A LEU* 4.4 14.1 - - + -
37A LEU* 4.5 6.5 - - + -
38A SER* 2.9 20.5 + - - -
40A VAL* 1.3 78.4 - - - +
42A VAL* 1.3 56.6 + - - +
44A ARG* 3.3 2.1 + - - +
45A TYR* 2.8 31.2 + - - +
97A GLU* 4.5 8.0 + - - -
101A THR* 3.2 25.1 + - - +
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 5.1 1.6 - - - -
37A LEU* 4.0 25.8 - - + -
38A SER 3.1 12.7 + - - +
39A ILE* 3.6 9.6 - - + +
40A VAL 3.3 0.2 - - - -
41A THR* 1.3 75.2 - - - +
43A TYR* 1.3 57.7 + - - +
45A TYR* 3.1 9.0 + - - +
46A LEU* 2.8 35.9 + - + +
60A PHE* 3.6 37.2 - - + -
63A LEU* 3.9 17.7 - - + -
69A ILE* 3.9 25.4 - - + -
77B ALA* 5.6 0.2 - - + -
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Residues in contact with TYR 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE 2.9 15.4 + - - +
40A VAL* 3.6 13.7 - - + -
42A VAL* 1.3 76.8 - - - +
44A ARG* 1.3 67.2 + - + +
46A LEU* 3.1 12.2 + - - +
47A THR* 3.0 37.7 + - - -
72B LEU* 4.7 5.2 - - + -
77B ALA* 4.0 21.3 - - + +
80B ALA* 3.9 24.5 - - + -
81B ALA 3.9 12.8 - - - -
84B GLU* 2.2 32.8 + - - -
96B MET* 3.2 44.0 - - + +
99B ILE* 3.8 7.7 - - + +
100B ILE* 4.1 17.0 - - + -
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Residues in contact with ARG 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER* 3.4 24.9 - - - -
15A ILE* 4.5 3.3 - - - +
40A VAL 3.0 14.8 + - - +
43A TYR* 1.3 84.5 - - + +
45A TYR* 1.3 62.9 + - - +
47A THR* 3.5 10.0 + - - +
48A ALA* 3.4 17.7 + - - +
95A ASP* 4.2 9.3 + - - -
97A GLU* 2.8 56.7 + - + +
84B GLU* 3.0 39.9 + - - -
94B LEU 5.3 1.6 + - - -
95B ASP* 4.4 3.2 - - - +
96B MET* 3.6 34.3 - - - +
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Residues in contact with TYR 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER* 4.1 2.5 - - - +
14A LEU* 3.7 41.7 - - + -
15A ILE* 3.7 35.2 - - + -
18A HIS* 3.0 42.4 + + + -
41A THR 2.8 21.5 + - - +
42A VAL 3.3 3.1 - - - +
44A ARG* 1.3 71.8 - - - +
46A LEU* 1.3 61.8 + - + +
48A ALA* 3.2 6.2 + - - +
49A ARG* 2.9 32.2 + - + +
59A GLU* 3.0 27.4 + - + -
63A LEU* 3.9 27.1 - - + -
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Residues in contact with LEU 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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42A VAL* 2.8 27.9 + - + +
43A TYR* 3.1 11.4 + - - +
45A TYR* 1.3 82.9 - - + +
47A THR* 1.3 51.5 + - - +
49A ARG* 3.2 4.6 + - + +
50A ALA* 2.8 36.4 + - - +
56A ILE* 3.8 30.7 - - + +
59A GLU* 3.8 28.3 - - + -
60A PHE* 3.6 31.2 - - + +
63A LEU* 4.2 6.5 - - + -
77B ALA* 4.6 7.6 - - + +
78B ILE* 4.4 7.6 - - + -
81B ALA* 3.6 13.0 - - + +
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Residues in contact with THR 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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43A TYR* 3.0 24.9 + - - -
44A ARG* 3.5 14.5 - - - +
46A LEU* 1.3 76.0 - - - +
48A ALA* 1.3 60.8 + - - +
51A TYR* 3.4 20.6 + - - +
81B ALA* 3.4 24.5 - - - +
84B GLU* 3.8 34.5 - - + +
85B ALA* 3.5 16.5 - - - +
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Residues in contact with ALA 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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15A ILE* 3.5 38.8 - - + -
44A ARG 3.4 3.1 + - - +
45A TYR* 3.2 9.9 + - + +
47A THR* 1.3 77.0 - - - +
49A ARG* 1.3 63.8 + - - +
50A ALA 3.2 1.0 + - - -
51A TYR* 3.8 15.9 + - - +
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Residues in contact with ARG 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 TYR* 2.9 33.3 + - + +
46A LEU* 3.2 9.8 + - + +
48A ALA* 1.3 73.6 - - - +
50A ALA* 1.3 66.3 + - - +
51A TYR 4.1 0.6 - - - +
54A LYS* 3.5 27.5 + - + +
56A ILE* 5.9 2.0 - - + -
59A GLU* 4.5 19.3 - - + +
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Residues in contact with ALA 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 LEU 2.8 16.4 + - - +
47A THR 3.6 5.6 - - - +
48A ALA 3.2 0.2 - - - -
49A ARG* 1.3 78.7 - - - +
51A TYR* 1.4 72.5 + - - +
54A LYS* 3.8 30.3 + - + +
56A ILE* 3.6 26.7 - - + -
81B ALA 4.2 2.7 - - - +
82B GLN* 5.0 1.1 - - - -
85B ALA* 3.7 13.0 - - + -
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Residues in contact with TYR 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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47A THR 3.4 13.4 + - - +
48A ALA* 4.1 11.0 - - - +
49A ARG 3.7 3.5 - - - +
50A ALA* 1.4 91.5 - - - +
54A LYS* 4.6 6.8 + - - -
85B ALA* 3.7 21.1 - - + +
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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