Contacts of the helix formed by residues 57 - 73 (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 SER 57 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA* 4.1 2.0 - - - -
50A MET* 3.5 39.1 - - - +
51A PRO 5.4 0.3 + - - -
52A ASN 4.3 2.3 + - - -
53A LYS* 3.4 18.3 - - - -
54A THR* 2.8 38.9 + - - +
56A HIS* 1.3 78.4 - - - +
58A TYR* 1.3 63.0 + - - +
60A TYR* 3.1 13.0 + - - +
61A ILE 4.0 0.2 + - - -
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Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP* 5.5 0.7 - - - -
39A ASN* 3.4 39.9 + - + -
42A TYR* 3.6 34.1 - - + -
43A HIS* 3.2 32.3 + + - +
46A ALA* 4.2 4.3 - - - +
54A THR 4.6 1.2 + - - -
55A ASP 3.2 20.9 - - - -
56A HIS* 4.1 4.9 - + - -
57A SER* 1.3 75.7 - - - +
59A HIS* 1.3 104.6 + + - +
60A TYR 3.0 1.0 + - - -
61A ILE* 3.0 14.0 + - - +
62A LYS* 3.1 32.3 + - + +
96A ASP* 4.8 7.8 + - - -
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Residues in contact with HIS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A HIS* 3.2 40.9 - + + +
57A SER 3.2 0.8 + - - -
58A TYR* 1.3 115.1 + + - +
60A TYR* 1.3 56.4 + - - +
62A LYS* 3.3 9.5 + - - +
63A ARG* 3.0 26.2 + - - +
96A ASP* 6.1 0.4 - - - -
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Residues in contact with TYR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A MET* 3.7 30.7 - - + -
57A SER* 3.1 13.0 + - - +
58A TYR 3.0 0.4 - - - -
59A HIS* 1.3 77.2 - - - +
61A ILE* 1.3 65.0 + - + +
63A ARG* 3.2 26.9 + - - +
64A LEU* 3.0 58.3 + - + +
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Residues in contact with ILE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR* 3.7 23.8 - - + +
45A ILE* 3.7 26.0 - - + -
46A ALA* 3.8 25.6 - - + +
49A THR* 3.9 12.6 - - - +
50A MET* 4.0 15.7 - - + -
58A TYR* 3.0 8.0 + - - +
60A TYR* 1.3 77.3 - - + +
62A LYS* 1.3 51.7 + - - +
64A LEU* 3.2 21.2 + - + +
65A THR* 2.8 35.7 + - - -
108A LEU* 3.5 27.8 - - + +
112A MET* 4.3 4.7 - - + -
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Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASN* 4.4 10.9 - - - +
42A TYR* 3.6 34.1 - - + -
58A TYR* 3.1 35.4 + - + +
59A HIS* 3.5 12.3 - - - +
61A ILE* 1.3 76.1 - - - +
63A ARG* 1.3 59.1 + - - +
65A THR* 3.3 9.5 + - - -
66A GLU* 2.9 27.0 + - - +
93A MET* 3.1 36.8 + - - +
94A LEU* 3.6 23.7 + - + +
95A SER 3.1 20.2 + - - -
96A ASP* 5.1 0.4 - - - +
97A ASN 4.8 0.4 - - - +
98A GLU* 4.7 3.0 - - - +
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Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A HIS 3.0 13.9 + - - +
60A TYR* 3.2 30.1 + - + +
62A LYS* 1.3 74.9 - - - +
64A LEU* 1.3 61.5 + - + +
66A GLU* 3.3 21.4 + - - +
67A SER* 3.0 28.2 + - - -
94A LEU* 5.3 1.1 - - - -
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 3.0 59.6 + - + +
61A ILE* 3.2 11.6 + - + +
63A ARG* 1.3 77.8 - - + +
65A THR* 1.3 59.4 + - - +
67A SER* 3.5 5.9 + - - -
68A ALA* 2.8 29.8 + - - +
108A LEU* 3.8 10.3 - - + -
111A GLU* 3.5 19.9 - - + +
112A MET* 4.0 35.7 - - + -
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Residues in contact with THR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR* 3.7 8.6 - - - +
61A ILE 2.8 20.8 + - - -
62A LYS* 3.4 11.2 - - - -
63A ARG 3.2 0.2 - - - -
64A LEU* 1.3 74.7 - - - +
66A GLU* 1.3 58.6 + - - +
68A ALA* 3.2 4.1 + - - +
69A ALA* 2.9 29.3 + - - +
89A TYR* 4.0 5.6 - - - +
93A MET* 3.7 18.2 - - + -
104A GLU* 3.6 33.9 - - + +
107A MET* 4.4 5.8 - - + +
108A LEU* 3.4 24.8 - - + +
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS 2.9 14.1 + - - +
63A ARG* 3.3 25.7 + - - +
65A THR* 1.3 74.4 - - - +
67A SER* 1.3 63.4 + - - +
69A ALA* 3.2 4.2 + - - +
70A ARG* 2.9 60.0 + - - +
90A LEU* 3.9 11.1 - - + +
93A MET* 3.5 16.9 - - + +
94A LEU* 4.2 24.2 - - + +
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Residues in contact with SER 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ARG* 3.0 13.6 + - - -
64A LEU* 3.7 6.3 - - - -
66A GLU* 1.3 82.9 - - - +
68A ALA* 1.3 62.5 + - - +
70A ARG* 3.6 16.0 + - - +
71A LYS* 3.4 22.7 + - - +
111A GLU* 2.6 25.1 + - - -
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU 2.8 19.7 + - - +
65A THR* 3.5 7.9 - - - +
66A GLU 3.2 0.2 - - - -
67A SER* 1.3 74.5 - - - +
69A ALA* 1.3 66.6 + - - +
71A LYS 3.0 3.6 + - - -
72A TYR* 2.9 29.9 + - + -
107A MET* 3.6 24.0 - - + +
108A LEU 4.4 0.7 - - - +
111A GLU* 3.4 30.2 - - + -
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Residues in contact with ALA 69 (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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65A THR 2.9 16.3 + - - +
66A GLU 3.2 5.1 + - - +
68A ALA* 1.3 75.5 - - - +
70A ARG* 1.3 62.0 + - - +
73A TYR* 2.7 38.7 + - + +
74A GLN* 4.5 0.7 + - - +
86A LEU* 3.7 6.0 - - + +
89A TYR* 3.8 28.7 - - + -
90A LEU* 4.0 9.0 - - + -
107A MET* 3.7 16.3 - - - -
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Residues in contact with ARG 70 (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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66A GLU* 2.9 45.9 + - - +
67A SER* 3.8 10.3 - - - +
68A ALA 3.2 0.4 - - - -
69A ALA* 1.3 75.6 - - - +
71A LYS* 1.3 62.0 + - + +
74A GLN* 6.0 1.6 - - - +
86A LEU* 4.1 26.8 - - + +
87A GLU* 5.6 5.3 - - - +
90A LEU* 3.3 30.6 - - + +
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Residues in contact with LYS 71 (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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67A SER* 3.4 19.8 + - - +
68A ALA 3.0 5.6 + - - +
70A ARG* 1.3 84.8 - - + +
72A TYR* 1.3 82.8 + - + +
75A GLU* 3.0 16.1 - - - +
111A GLU* 2.5 37.1 + - - -
140C THR* 6.2 3.5 - - + +
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Residues in contact with TYR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ALA* 2.9 25.2 + - - +
71A LYS* 1.3 102.8 + - + +
73A TYR* 1.3 67.7 + - - +
74A GLN 3.3 2.5 - - - -
75A GLU* 3.1 14.5 + - - +
76A GLU* 3.0 39.3 + - - +
107A MET* 4.0 15.9 - - + -
110A LYS* 3.8 49.4 + - + +
111A GLU* 3.8 26.5 + - + -
140C THR* 6.6 0.2 - - + -
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Residues in contact with TYR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA* 2.7 34.7 + - + +
72A TYR* 1.3 72.0 - - - +
74A GLN* 1.3 74.8 + - - +
76A GLU* 3.1 10.7 + - - -
79A ALA* 3.4 37.8 + - + +
82A VAL* 3.3 23.8 - - + +
84A LEU 2.7 31.5 + - - -
86A LEU* 3.8 33.2 - - + -
89A TYR* 3.5 40.0 - + + +
103A LEU* 4.1 8.7 - - + -
107A MET* 3.9 15.5 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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