Contacts of the helix formed by residues 37 - 49 (chain D) in PDB entry 2H1O
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 ALA 37 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C PHE* 3.2 34.5 - - + +
79C ASP* 3.7 20.0 - - - +
80C GLU* 3.8 5.6 - - - +
83C ALA* 4.0 2.0 - - + +
36D SER* 1.3 70.7 + - - +
38D ILE* 1.3 51.8 + - + +
40D VAL* 3.1 5.3 + - - +
41D ALA* 2.6 36.6 + - - +
75D ILE* 3.9 14.6 - - + +
76D LEU 3.1 17.8 + - - +
77D PRO* 4.5 0.7 - - + -
78D PHE 5.0 0.9 - - - +
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Residues in contact with ILE 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ILE* 4.9 3.6 - - + -
78C PHE* 3.8 23.1 - - + -
106C TYR* 3.8 40.6 - - + +
6D THR* 5.8 0.7 - - - +
36D SER* 2.9 13.4 - - - +
37D ALA* 1.3 77.8 - - - +
39D THR* 1.3 63.3 + - - +
41D ALA* 3.1 12.6 + - - +
42D GLU* 3.2 18.7 + - + +
78D PHE* 4.7 14.4 - - + -
103D ALA* 4.9 2.9 - - - +
106D TYR* 3.8 30.7 - - + -
107D ILE* 4.0 19.7 - - + -
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Residues in contact with THR 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU 4.2 9.2 + - - +
6D THR* 3.1 50.4 + - + +
9D ILE* 4.2 14.8 - - + -
35D LEU* 4.6 5.4 - - + -
36D SER* 2.7 23.3 + - - -
38D ILE* 1.3 76.5 - - - +
40D VAL* 1.3 62.3 + - - +
41D ALA 3.2 0.2 + - - -
42D GLU* 3.2 4.8 + - - +
43D MET* 3.0 25.8 + - + +
107D ILE* 3.9 18.4 - - - +
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Residues in contact with VAL 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C GLU* 5.1 2.9 - - + -
83C ALA* 4.6 3.8 - - + -
35D LEU* 3.9 26.0 - - + -
36D SER 2.7 21.3 + - - +
37D ALA* 3.5 8.5 - - - +
39D THR* 1.3 73.2 - - - +
41D ALA* 1.3 61.5 + - - +
43D MET* 3.5 8.0 + - + +
44D ARG* 3.1 38.3 + - + +
68D LEU* 4.0 30.3 - - + -
75D ILE* 3.6 30.7 - - + -
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Residues in contact with ALA 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C PHE* 3.7 20.0 - - + -
83C ALA* 4.0 12.6 - - + -
86C TYR* 3.4 30.9 - - + -
106C TYR* 4.8 1.3 - - + -
37D ALA 2.6 17.0 + - - +
38D ILE* 3.1 10.0 + - - +
40D VAL* 1.3 75.5 - - - +
42D GLU* 1.3 60.2 + - - +
44D ARG* 3.5 2.8 + - - +
45D LEU* 2.9 28.6 + - - +
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Residues in contact with GLU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C TYR* 2.8 32.7 + - - -
90C ARG* 4.7 3.2 + - - -
102C ALA* 4.6 3.2 - - - +
106C TYR* 3.0 23.5 + - - +
6D THR* 4.4 17.9 - - + +
38D ILE* 3.2 15.6 + - + +
39D THR* 3.2 7.4 + - - +
41D ALA* 1.3 72.8 - - - +
43D MET* 1.3 61.3 + - - +
45D LEU* 3.8 12.9 - - - +
46D GLY* 2.8 26.9 + - - -
64H LEU* 4.4 8.6 - - + +
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Residues in contact with MET 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D THR* 5.1 4.9 - - + +
9D ILE* 3.9 45.3 - - + +
10D SER* 5.7 1.6 - - - -
13D LEU* 5.6 4.7 - - + -
35D LEU* 4.5 10.8 - - + -
39D THR* 3.0 22.8 + - + +
40D VAL* 3.6 15.7 - - + +
41D ALA 3.3 0.2 - - - -
42D GLU* 1.3 75.8 - - - +
44D ARG* 1.3 63.5 + - + +
46D GLY* 3.0 12.5 + - - -
47D VAL* 3.2 15.6 + - - +
63D MET* 3.4 37.7 - - + +
67D ILE* 4.4 7.4 - - + -
68D LEU* 4.3 15.7 - - + -
64H LEU* 3.7 19.4 - - + +
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Residues in contact with ARG 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C GLU* 3.0 45.2 + - - +
83C ALA* 4.1 3.5 - - - +
84C ALA* 3.6 33.8 - - - +
87C ALA* 3.6 15.3 - - + +
40D VAL* 3.1 22.8 + - - +
41D ALA* 3.8 2.7 - - - +
43D MET* 1.3 77.8 - - + +
45D LEU* 1.3 65.6 + - - +
47D VAL* 3.1 10.2 + - - +
48D ALA* 3.0 20.4 + - - +
63D MET* 4.6 5.6 - - + -
64D GLU* 3.1 39.4 + - - +
68D LEU* 3.3 25.2 - - + +
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Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C TYR* 3.6 28.9 - - + +
87C ALA* 3.5 28.0 - - - +
90C ARG* 3.7 37.0 - - + +
91C SER* 3.8 4.9 - - - +
41D ALA 2.9 18.0 + - - +
42D GLU* 3.8 14.6 - - - +
43D MET 3.3 0.2 - - - -
44D ARG* 1.3 75.6 - - - +
46D GLY* 1.3 64.7 + - - +
48D ALA* 2.9 12.2 + - - -
49D LEU* 2.9 41.8 + - + +
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Residues in contact with GLY 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D GLU 2.8 15.4 + - - -
43D MET 3.0 5.8 + - - -
45D LEU* 1.3 79.0 - - - +
47D VAL* 1.3 59.8 + - - +
49D LEU* 3.7 13.3 + - - +
50D LEU* 3.9 12.5 - - - +
63H GLU 5.0 1.3 - - - +
64H LEU* 3.7 31.0 - - - +
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Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D MET 3.2 11.4 + - - +
44D ARG* 3.1 9.7 + - - +
45D LEU 3.1 0.4 - - - -
46D GLY* 1.3 75.0 - - - +
48D ALA* 1.3 65.4 + - - +
50D LEU* 3.5 12.1 + - - +
56D LYS* 3.4 26.6 - - + +
59D LEU* 3.8 25.8 - - + -
60D HIS* 3.9 39.7 - - + +
63D MET* 3.9 26.7 - - + -
64H LEU* 5.0 3.4 - - + -
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Residues in contact with ALA 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C ALA* 3.8 13.5 - - + +
88C GLN* 5.4 0.4 - - - -
91C SER* 3.4 32.6 - - - +
44D ARG 3.0 12.6 + - - +
45D LEU 2.9 8.1 + - - +
47D VAL* 1.3 79.2 - - - +
49D LEU* 1.3 58.2 + - - +
50D LEU 3.0 13.3 + - - +
56D LYS* 4.3 6.3 + - - +
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Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ARG* 4.7 0.9 - - - +
91C SER* 3.6 30.3 - - - +
94C LYS* 4.1 26.9 - - + -
95C THR* 5.9 2.0 - - + -
45D LEU* 2.9 38.2 + - + +
46D GLY* 3.7 7.6 + - - +
47D VAL 3.3 1.0 - - - -
48D ALA* 1.3 74.0 - - - +
50D LEU* 1.3 62.2 + - - +
51D LEU* 4.1 2.8 + - - +
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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