Contacts of the helix formed by residues 54 - 68 (chain C) in PDB entry 3P3W
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 54 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A SER* 3.7 21.4 + - - +
91A ALA* 5.5 3.7 - - - +
51C ASP* 3.1 35.4 + - + +
52C SER 3.4 1.2 - - - +
53C SER* 1.3 77.9 + - - +
55C SER* 1.3 59.8 + - - +
56C PHE* 3.2 25.9 + - - +
57C SER* 3.2 33.5 + - - +
58C VAL* 3.6 6.1 - - - +
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Residues in contact with SER 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASN* 4.4 2.5 - - - -
84A THR* 4.1 25.2 + - - +
87A SER* 4.0 17.2 - - - -
88A PHE* 3.7 9.9 - - - -
52C SER 5.2 0.7 - - - -
53C SER 3.2 4.9 + - - -
54C ASN* 1.3 72.9 - - - +
56C PHE* 1.3 60.0 + - - +
57C SER 3.7 0.2 - - - -
58C VAL* 4.2 10.5 - - - +
59C THR* 3.4 17.8 + - - +
80C MET 4.0 14.4 + - - -
84C THR* 2.7 28.2 + - - +
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Residues in contact with PHE 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A SER* 4.4 3.7 - - - +
88A PHE* 3.5 54.1 - + - -
91A ALA* 3.9 20.6 - - + -
92A LEU* 3.4 35.4 - - + -
312A CYS 4.8 10.5 - - - -
313A LEU 4.5 1.6 - - - -
314A ALA* 4.1 33.2 - - + -
318A VAL* 5.2 2.2 - - + -
54C ASN* 3.1 21.4 - - - +
55C SER* 1.3 76.6 - - - +
57C SER* 1.3 65.0 + - - +
58C VAL 3.2 1.3 - - - -
59C THR* 2.7 21.3 + - - -
60C ASN* 3.2 8.2 + - + +
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Residues in contact with SER 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ALA* 4.9 3.6 - - - -
50C LEU* 4.5 4.8 - - - +
51C ASP* 3.1 44.9 + - - +
54C ASN* 3.2 13.5 + - - -
56C PHE* 1.3 79.6 - - - +
58C VAL* 1.3 59.0 + - - +
60C ASN* 3.4 8.0 + - - +
61C ALA* 2.8 32.6 + - - +
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Residues in contact with VAL 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 4.9 1.8 - - + +
50C LEU* 4.2 22.2 - - + -
51C ASP 3.7 12.1 - - - +
54C ASN 3.6 17.0 + - - +
55C SER* 4.2 9.6 - - - +
56C PHE 3.2 0.4 - - - -
57C SER* 1.3 77.3 + - - +
59C THR* 1.3 57.7 + - - +
61C ALA* 3.4 1.9 + - - +
62C PHE* 2.8 32.0 + - + +
81C SER* 3.8 21.3 - - - +
84C THR* 3.8 22.2 - - + -
85C LEU* 3.8 29.8 - - + -
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Residues in contact with THR 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A THR* 4.8 1.8 - - + -
88A PHE* 3.4 32.8 - - + -
55C SER 3.4 4.3 + - - +
56C PHE* 2.7 21.3 + - - -
58C VAL* 1.3 76.8 - - - +
60C ASN* 1.3 55.6 + - - +
62C PHE* 3.7 6.4 - - - +
63C CYS* 2.9 40.1 + - - -
84C THR* 3.6 24.0 - - + -
88C PHE* 3.8 27.8 - - + -
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Residues in contact with ASN 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A CYS 6.0 1.3 - - - -
313A LEU* 6.1 0.2 - - - +
314A ALA* 2.8 44.6 - - + +
315A ASN* 4.3 10.9 + - - +
56C PHE* 3.2 9.9 + - + +
57C SER* 3.5 8.3 - - - +
58C VAL 3.3 0.2 - - - -
59C THR* 1.3 80.3 + - - +
61C ALA* 1.3 55.8 + - - +
63C CYS* 4.0 2.8 - - - +
64C SER* 3.1 29.5 + - - -
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Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ASN* 5.9 0.2 - - - -
11C LEU* 4.6 3.4 - - + -
48C ASP* 3.6 26.2 - - + +
49C HIS 5.9 0.2 - - - -
50C LEU* 4.1 23.1 - - + -
57C SER 2.8 20.7 + - - +
58C VAL 3.9 2.9 - - - +
60C ASN* 1.3 72.8 - - - +
62C PHE* 1.3 59.7 + - - +
64C SER* 3.8 4.9 - - - -
65C GLN* 3.1 31.1 + - - +
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Residues in contact with PHE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 4.6 9.6 - - + +
58C VAL* 2.8 22.2 + - + +
59C THR* 3.7 6.3 - - - +
60C ASN 3.3 0.2 - - - -
61C ALA* 1.3 76.1 - - - +
63C CYS* 1.3 66.6 + - - +
65C GLN* 3.2 7.1 + - - +
66C PHE* 2.9 30.8 + + + +
73C ILE* 3.6 30.0 - - + +
84C THR* 6.4 0.4 - - + -
85C LEU* 4.5 17.3 - - + -
88C PHE* 3.5 55.9 - + + -
89C CYS* 4.0 21.1 - - - -
92C LEU* 3.7 17.9 - - + -
94C THR* 4.7 9.0 - - - -
312C CYS* 4.6 0.7 - - - -
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Residues in contact with CYS 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C THR* 2.9 23.5 + - - +
60C ASN* 4.3 3.8 - - - +
62C PHE* 1.3 79.1 - - - +
64C SER* 1.3 57.6 + - - +
66C PHE* 3.8 3.4 - - - +
67C SER* 2.7 36.3 + - - +
88C PHE* 4.5 7.9 - - - -
312C CYS* 2.0 55.5 - - + +
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Residues in contact with SER 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A ASN* 4.0 20.6 + - - -
48C ASP* 4.3 12.5 + - - -
60C ASN 3.1 19.6 + - - -
61C ALA* 3.8 8.7 - - - -
62C PHE 3.2 0.2 - - - -
63C CYS* 1.3 78.0 - - - +
65C GLN* 1.3 61.3 + - - +
67C SER* 4.2 4.9 - - - -
68C ARG* 3.6 34.1 + - - +
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Residues in contact with GLN 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C GLY* 2.7 27.9 - - - -
10C GLY 2.9 27.3 + - - -
11C LEU* 3.3 17.5 - - + -
46C HIS* 3.0 23.0 + - - +
48C ASP* 2.8 20.8 + - - +
61C ALA 3.1 18.6 + - - +
62C PHE* 3.2 9.5 + - - +
64C SER* 1.3 78.9 - - - +
66C PHE* 1.3 60.7 + - - +
68C ARG* 3.4 10.2 + - - +
69C GLY 3.2 12.1 + - - -
70C VAL* 3.4 22.4 + - + +
73C ILE* 4.3 14.4 - - + -
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Residues in contact with PHE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C PHE* 2.9 25.2 + + + +
63C CYS* 4.1 8.1 - - - +
65C GLN* 1.3 73.1 - - - +
67C SER* 1.3 58.3 + - - +
69C GLY* 2.4 34.7 + - - +
70C VAL* 4.8 2.7 - - - +
73C ILE* 5.4 2.7 - - + -
92C LEU* 3.7 40.4 - - + -
93C HIS 5.1 0.9 - - - -
94C THR* 3.2 35.0 - - + -
310C GLY 3.6 28.2 + - - -
311C ASP 3.7 22.7 - - - -
312C CYS* 5.0 2.2 - - - -
318C VAL* 5.5 6.3 - - + -
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Residues in contact with SER 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C CYS* 2.7 24.0 + - - +
64C SER* 4.2 5.8 - - - -
65C GLN 3.5 0.4 - - - -
66C PHE* 1.3 76.0 - - - +
68C ARG* 1.3 62.3 + - - +
69C GLY* 3.1 1.2 + - - -
310C GLY* 3.3 29.8 + - - -
311C ASP* 5.3 1.0 - - - -
312C CYS* 5.6 1.4 + - - +
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Residues in contact with ARG 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C SER* 5.5 1.4 + - - -
46C HIS* 3.8 27.5 - - + +
47C VAL 5.7 1.4 + - - +
48C ASP* 5.5 7.9 + - - -
64C SER* 3.6 22.9 + - - +
65C GLN* 3.4 13.8 + - - +
67C SER* 1.3 79.9 - - - +
69C GLY* 1.3 63.2 + - - +
70C VAL* 3.4 12.7 + - + +
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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