Contacts of the helix formed by residues 39 - 50 (chain A) in PDB entry 3PHW
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 ASN 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ASP* 3.0 11.9 + - - +
38A GLY* 1.3 79.5 + - - +
40A CYS* 1.3 66.5 + - - +
41A PHE 3.1 3.4 - - - -
42A TYR* 2.9 13.4 + - + -
43A HIS* 2.9 37.0 + - + +
58A TYR* 3.4 42.1 + - + -
62A LYS* 4.4 8.9 - - - +
96A ASP* 5.0 0.7 - - - +
97A ASN* 3.2 46.3 + - - +
98A GLU 4.0 3.8 + - - +
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Residues in contact with CYS 40 (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 GLN* 4.2 2.6 - - + +
35A PRO 3.6 18.2 - - - +
37A ASP* 3.6 1.2 + - - -
39A ASN* 1.3 76.4 - - - +
41A PHE* 1.3 58.8 + - - +
43A HIS* 3.5 13.9 - - - +
44A SER* 2.8 34.2 + - - -
151A HIS* 3.9 8.7 - - + -
152A PHE* 3.5 32.3 - - - +
75B GLY 3.4 7.2 - - - -
76B NEH 1.8 62.4 - - + +
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Residues in contact with PHE 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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39A ASN 3.0 1.2 + - - -
40A CYS* 1.3 80.5 - - - +
42A TYR* 1.3 82.9 + + + +
44A SER* 3.3 3.8 + - - -
45A ILE* 3.1 40.1 + - + +
100A GLY* 3.8 24.5 - - - +
101A SER 3.6 23.3 - - - -
104A GLU* 3.8 18.2 - - + -
105A ALA* 3.7 25.4 - - + -
108A LEU* 4.2 11.2 - - + -
118A ILE* 4.6 1.3 - - + -
144A LEU* 3.8 23.8 - - + -
152A PHE* 3.7 38.8 - + + -
75B GLY 4.2 0.9 - - - +
76B NEH 3.9 0.2 - - - +
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Residues in contact with TYR 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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39A ASN* 2.9 17.6 + - + +
41A PHE* 1.3 90.0 - + + +
43A HIS* 1.3 66.6 + - - +
45A ILE 3.5 0.4 + - - +
46A ALA* 3.0 25.5 + - - +
58A TYR* 3.6 25.3 - - + +
61A ILE* 3.7 25.5 - - + +
62A LYS* 3.6 38.5 - - + -
65A THR* 3.7 20.0 - - - -
93A MET* 3.7 16.4 + - - +
98A GLU 4.0 10.5 + - - -
99A TRP 4.5 1.6 + - - -
100A GLY* 3.7 28.1 + - - -
104A GLU* 3.5 21.0 - - + +
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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
----------------------------------------------------------
34A GLN* 3.2 23.4 + - + +
35A PRO* 4.0 22.8 - - + +
37A ASP* 3.3 28.5 + - - -
39A ASN* 2.9 38.9 + - + +
40A CYS* 3.5 9.4 - - - +
42A TYR* 1.3 79.0 - - - +
44A SER* 1.3 54.9 + - - +
46A ALA* 3.3 4.1 + - - +
47A GLU* 2.8 30.0 + - - +
53A LYS* 3.7 7.7 + - - +
54A THR 4.7 0.4 + - - -
55A ASP* 3.3 23.4 + - + -
58A TYR* 3.2 33.4 + + + +
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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
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34A GLN* 3.3 10.6 - - - +
40A CYS 2.8 22.0 + - - -
41A PHE 3.5 5.2 - - - -
43A HIS* 1.3 73.6 - - - +
45A ILE* 1.3 68.3 + - - +
47A GLU* 3.2 11.5 + - - +
48A LEU* 3.3 16.5 + - - +
144A LEU* 3.8 25.4 - - - -
152A PHE* 3.3 10.3 + - - -
153A ASP* 3.1 27.5 - - - -
154A ALA* 3.9 3.3 - - - +
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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
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41A PHE* 3.1 32.8 + - + +
42A TYR 3.9 4.9 - - - +
43A HIS 3.4 0.2 - - - -
44A SER* 1.3 75.5 - - - +
46A ALA* 1.3 58.7 + - - +
48A LEU* 2.9 13.3 + - - +
49A THR* 2.8 31.0 + - + +
61A ILE* 3.7 33.9 - - + -
108A LEU* 4.5 2.0 - - + -
112A MET* 4.3 13.9 - - - -
114A ILE* 5.3 0.7 - - + -
116A ILE* 3.8 29.4 - - + -
142A VAL* 3.9 19.7 - - + -
144A LEU* 4.3 14.4 - - + -
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Residues in contact with ALA 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 TYR 3.0 18.1 + - - +
43A HIS* 3.5 5.4 - - - +
45A ILE* 1.3 75.7 - - - +
47A GLU* 1.3 64.2 + - - +
49A THR* 3.7 6.5 - - - -
50A MET* 2.9 50.2 + - - +
53A LYS* 3.9 6.6 - - + +
57A SER* 4.1 16.2 - - - -
58A TYR 4.2 6.5 - - - +
61A ILE* 3.8 9.3 - - + +
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Residues in contact with GLU 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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32A VAL* 3.4 19.3 - - + +
34A GLN* 3.0 30.0 + - - +
43A HIS 2.8 16.9 + - - +
44A SER 3.4 11.0 - - - +
45A ILE 3.2 0.4 - - - -
46A ALA* 1.3 73.5 - - - +
48A LEU* 1.3 57.6 + - - +
50A MET 4.4 6.4 - - - +
53A LYS* 3.2 32.5 + - - +
154A ALA* 3.9 13.2 - - + -
156A ARG* 3.2 37.0 + - - +
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Residues in contact with LEU 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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32A VAL* 5.9 0.2 - - + -
44A SER 3.3 5.4 + - - +
45A ILE 2.9 8.2 + - - +
47A GLU* 1.3 79.2 - - + +
49A THR* 1.3 62.0 + - - +
142A VAL* 3.7 33.7 - - + +
143A ASN 3.3 31.2 - - - +
144A LEU* 4.2 3.8 - - + -
154A ALA* 3.9 18.8 - - + -
155A LEU 3.5 9.9 - - - +
156A ARG* 3.5 44.9 + - + +
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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
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45A ILE* 2.8 33.5 + - + +
46A ALA* 3.7 4.2 - - - -
48A LEU* 1.3 82.8 - - - +
50A MET* 1.3 67.9 + - - +
51A PRO* 3.8 6.8 - - - +
61A ILE* 3.9 4.5 - - - +
112A MET* 3.8 25.1 - - + -
114A ILE* 4.5 7.6 - - + -
142A VAL* 3.8 23.8 - - + -
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Residues in contact with MET 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 ALA* 2.9 28.0 + - - +
47A GLU 4.4 4.5 + - - +
48A LEU 3.9 0.2 - - - -
49A THR* 1.3 88.9 - - - +
51A PRO* 1.3 75.7 - - + +
53A LYS* 3.4 20.7 + - + +
57A SER* 3.5 40.2 - - - +
60A TYR* 3.7 29.2 - - + -
61A ILE* 4.0 15.5 - - + -
112A MET* 6.4 0.2 - - + -
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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