Contacts of the helix formed by residues 78 - 93 (chain A) 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 ASP 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A MET* 4.4 6.4 - - + -
52A SER* 2.7 33.9 + - - +
53A SER* 4.9 0.9 + - - -
77A TYR* 1.3 73.6 - - - +
79A GLN* 1.3 65.1 + - - +
80A MET* 3.4 26.0 + - - +
81A SER* 2.7 24.1 + - - -
82A MET* 3.1 23.6 + - - +
101A PHE* 3.6 11.4 - - - -
140A GLU* 4.4 12.6 - - - +
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Residues in contact with GLN 79 (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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78A ASP* 1.3 77.9 - - - +
80A MET* 1.3 66.1 + - + +
82A MET* 4.0 15.0 - - + +
83A ASN* 4.8 2.8 + - - +
101A PHE* 4.0 15.8 - - + -
139A THR* 3.4 35.7 + - - +
140A GLU* 4.3 14.6 + - - +
142A GLY* 6.3 0.9 - - - -
143A PHE* 3.3 37.2 - - - -
143C PHE* 4.5 12.4 - - - -
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Residues in contact with MET 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A SER 5.0 1.1 - - - +
53A SER* 3.5 36.6 - - - +
78A ASP* 3.2 15.5 + - - +
79A GLN* 1.3 83.6 - - + +
81A SER* 1.3 65.2 + - - +
82A MET 3.4 0.5 + - - -
83A ASN* 4.2 7.1 + - - +
84A THR* 4.3 4.3 + - - -
83C ASN* 3.2 50.0 + - - +
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Residues in contact with SER 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A MET* 5.7 0.7 - - - -
52A SER* 2.8 37.2 + - - -
55A SER* 5.2 2.4 - - - -
58A VAL* 3.2 26.1 - - - +
76A PHE 5.4 0.4 - - - -
77A TYR* 4.0 13.5 - - - -
78A ASP* 2.7 17.8 + - - -
80A MET* 1.3 71.4 - - - +
82A MET* 1.3 63.0 + - - +
83A ASN 3.5 0.2 - - - -
84A THR* 3.4 8.9 + - - -
85A LEU* 3.2 25.8 + - - +
83C ASN* 5.1 1.5 + - - +
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Residues in contact with MET 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR* 3.6 29.9 - - + +
78A ASP 3.1 21.4 + - - +
79A GLN* 4.0 11.2 - - + +
80A MET 3.3 1.0 - - - -
81A SER* 1.3 78.1 - - - +
83A ASN* 1.3 86.9 + - + +
84A THR 3.3 1.0 + - - -
85A LEU* 4.2 0.9 - - - +
86A THR* 3.0 31.0 + - + +
101A PHE* 3.7 23.8 - - - -
103A THR* 3.7 30.1 - - + -
104A ASP 5.5 1.8 - - - +
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Residues in contact with ASN 83 (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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79A GLN 4.8 1.8 + - - +
80A MET 4.2 6.9 + - - +
81A SER 3.5 0.4 - - - -
82A MET* 1.3 97.3 - - + +
84A THR* 1.3 58.3 + - - +
86A THR* 3.3 10.1 + - - -
87A SER* 2.7 36.3 + - - -
53C SER 4.0 6.1 - - - +
55C SER* 4.4 2.8 - - - -
80C MET* 3.4 45.6 - - + +
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Residues in contact with THR 84 (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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55A SER* 3.6 19.5 + - - +
58A VAL* 5.4 7.2 - - + -
59A THR* 3.7 19.5 - - + -
80A MET 4.3 9.0 + - - -
81A SER* 3.4 9.5 + - - -
82A MET 3.2 0.8 - - - -
83A ASN* 1.3 77.7 - - - +
85A LEU* 1.3 66.7 + - + +
87A SER* 3.2 3.1 + - - -
88A PHE* 3.1 52.1 + - + -
55C SER* 4.1 19.6 + - - +
80C MET 5.5 1.4 + - - -
83C ASN* 4.5 4.9 + - - +
84C THR* 4.8 4.2 + - + +
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Residues in contact with LEU 85 (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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11A LEU* 4.4 13.5 - - + -
58A VAL* 3.8 32.3 - - + +
59A THR* 6.0 0.4 - - - -
62A PHE* 4.0 35.0 - - + -
76A PHE 3.9 21.3 - - - +
77A TYR* 4.2 9.9 - - + -
81A SER* 3.2 13.8 + - - +
82A MET 4.3 1.6 - - - +
84A THR* 1.3 79.9 - - + +
86A THR* 1.3 61.2 + - - +
88A PHE* 4.1 4.5 - - + +
89A CYS* 3.3 30.5 + - - -
96A PHE* 4.0 31.6 - - + -
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Residues in contact with THR 86 (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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77A TYR* 4.8 8.3 - - + -
82A MET* 3.0 22.6 + - + +
83A ASN* 3.3 12.5 + - - -
85A LEU* 1.3 77.8 - - + +
87A SER* 1.3 61.4 + - - +
89A CYS* 3.8 1.6 + - - +
90A GLY* 3.2 21.1 + - - -
96A PHE* 5.8 0.9 - - + -
103A THR* 4.3 23.1 - - + -
107A VAL* 4.1 20.6 - - + +
108A GLN 4.1 8.3 + - - +
110A VAL* 3.8 32.3 - - + -
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Residues in contact with SER 87 (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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83A ASN* 2.7 29.7 + - - -
84A THR 3.2 4.8 + - - -
86A THR* 1.3 80.3 + - - +
88A PHE* 1.3 62.7 + - - +
90A GLY* 3.3 10.2 + - - -
91A ALA* 3.4 14.0 + - - +
53C SER 4.6 2.3 + - - -
54C ASN* 3.7 27.5 + - - +
55C SER* 4.0 16.6 + - - -
56C PHE* 4.1 3.2 - - - -
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Residues in contact with PHE 88 (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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59A THR* 3.9 15.7 - - + -
62A PHE* 3.6 37.6 - + + -
63A CYS* 4.8 6.1 - - - -
84A THR* 3.1 48.0 + - + +
85A LEU* 4.1 6.3 - - + +
87A SER* 1.3 76.5 - - - +
89A CYS* 1.3 58.8 + - - +
91A ALA 3.6 0.2 + - - -
92A LEU* 3.1 32.7 + - - +
312A CYS* 4.8 14.1 - - + -
55C SER* 3.7 18.2 - - - -
56C PHE* 3.5 33.9 - + - -
59C THR* 3.4 31.6 - - + -
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Residues in contact with CYS 89 (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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62A PHE* 3.6 25.4 - - - -
73A ILE* 5.1 1.3 - - - -
85A LEU 3.3 18.4 + - - +
86A THR* 4.1 4.3 - - - +
87A SER 3.3 0.2 - - - -
88A PHE* 1.3 76.9 - - - +
90A GLY* 1.3 59.9 + - - +
91A ALA 3.2 0.9 - - - -
93A HIS* 3.1 23.0 + - - -
94A THR* 3.1 34.8 + - - +
95A SER 4.9 0.2 - - - -
96A PHE* 3.6 26.5 - - + -
109A PHE* 3.4 20.1 - - + +
110A VAL* 5.1 0.4 - - + -
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Residues in contact with GLY 90 (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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86A THR 3.2 15.8 + - - -
87A SER* 3.3 6.0 + - - -
88A PHE 3.3 0.6 - - - -
89A CYS* 1.3 78.9 - - - +
91A ALA* 1.3 55.7 + - - +
93A HIS* 3.8 18.1 + - - -
108A GLN* 4.1 16.2 - - - +
109A PHE* 4.6 6.0 - - - -
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Residues in contact with ALA 91 (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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87A SER 3.4 6.7 + - - +
90A GLY* 1.3 76.8 - - - +
92A LEU* 1.3 59.1 + - - +
93A HIS* 3.1 27.7 + - - -
318A VAL* 3.3 13.5 - - + +
54C ASN* 5.5 3.6 - - - +
56C PHE* 3.9 34.8 - - + -
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Residues in contact with LEU 92 (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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62A PHE* 3.7 19.1 - - + -
66A PHE* 3.7 36.1 - - + -
88A PHE 3.1 15.3 + - - +
91A ALA* 1.3 74.4 - - - +
93A HIS* 1.3 69.4 - - - +
94A THR* 3.4 13.5 + - - +
311A ASP 4.4 9.6 - - - +
312A CYS* 3.7 28.9 - - - -
313A LEU 5.4 0.7 - - - +
318A VAL* 3.2 29.8 - - + -
322A GLN* 3.8 15.6 - - - +
56C PHE* 3.4 27.6 - - + -
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Residues in contact with HIS 93 (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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89A CYS 3.1 10.4 + - - -
90A GLY 3.8 16.4 + - - -
91A ALA* 3.1 19.5 + - - -
92A LEU* 1.3 79.2 - - - +
94A THR* 1.3 60.1 + - - +
109A PHE* 3.2 35.7 - + + -
318A VAL* 3.8 4.6 - - + +
319A PRO 3.6 23.9 + - - -
320A TRP* 4.5 7.0 - - - +
322A GLN* 4.0 4.6 - - + +
323A GLY* 3.1 30.5 - - - -
324A ILE* 3.4 22.6 - - + +
326A ILE* 5.0 1.6 - - - +
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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