Contacts of the helix formed by residues 86 - 103 (chain B) in PDB entry 1PN9
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 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B PRO* 3.4 2.3 - - + +
85B LYS* 1.3 76.5 - - - +
87B PRO* 1.3 68.6 - - - +
88B GLN* 3.5 10.8 + - - +
89B LYS* 3.0 47.0 + - + +
90B ARG* 2.8 33.1 + - - +
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Residues in contact with PRO 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A TYR* 3.7 10.7 - - + +
74A GLU* 4.2 25.3 - - + +
75A LYS* 4.1 38.6 - - + +
85B LYS 3.0 9.6 - - - +
86B ASP* 1.3 91.4 - - - +
88B GLN* 1.3 56.5 + - - +
90B ARG* 3.4 2.2 + - + +
91B ALA* 2.9 29.3 + - - +
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Residues in contact with GLN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASP 5.4 0.3 - - - +
60A PHE* 3.5 50.5 - - + +
71A TYR* 4.0 16.9 + - + -
75A LYS* 4.8 6.6 + - - +
86B ASP* 3.3 11.6 + - - +
87B PRO* 1.3 75.7 - - - +
89B LYS* 1.3 67.6 + - + +
91B ALA* 3.1 13.7 + - - +
92B VAL* 3.3 15.2 + - + +
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Residues in contact with LYS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PRO* 3.9 27.4 - - + +
86B ASP* 3.0 32.8 + - + +
88B GLN* 1.3 77.4 - - + +
90B ARG* 1.3 61.8 + - - +
92B VAL* 3.5 10.7 + - - +
93B VAL* 3.4 23.6 + - - +
148B ALA* 5.1 6.9 - - - +
151B ASP* 4.4 14.1 + - - -
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Residues in contact with ARG 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ILE* 5.3 0.2 - - - -
74A GLU* 3.5 32.2 + - - +
90A ARG* 3.7 7.1 - - - +
74B GLU* 3.2 24.7 + - - +
80B ASP* 5.3 1.0 + - - -
83B TYR* 2.9 58.3 + - + +
84B PRO* 2.7 31.8 + - - +
85B LYS* 3.5 22.8 + - - +
86B ASP 2.8 15.2 + - - +
87B PRO 3.8 4.5 - - - +
89B LYS* 1.3 74.8 - - - +
91B ALA* 1.3 60.5 - - - +
93B VAL* 3.2 5.1 + - - +
94B ASN* 2.8 41.9 + - - +
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Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PHE* 4.0 3.4 - - + -
62A LEU* 3.7 33.4 - - + +
67A ALA* 4.1 4.2 - - - +
71A TYR* 3.9 16.8 - - + +
74A GLU* 6.0 0.2 - - - -
87B PRO 2.9 17.1 + - - +
88B GLN 3.1 6.5 + - - +
90B ARG* 1.3 76.9 - - - +
92B VAL* 1.3 56.5 + - - +
94B ASN* 3.2 9.5 + - - +
95B GLN* 2.8 31.4 + - - +
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE* 3.8 22.7 - - + -
62A LEU* 4.8 2.0 - - + -
88B GLN* 3.3 14.3 + - + +
89B LYS* 3.7 9.0 - - - +
90B ARG 3.2 0.8 - - - -
91B ALA* 1.3 77.6 - - - +
93B VAL* 1.3 63.3 + - - +
95B GLN* 3.3 7.7 + - - +
96B ARG* 2.9 43.1 + - - +
148B ALA* 3.4 34.1 - - + +
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TYR* 3.8 26.9 - - + -
84B PRO* 4.3 14.1 - - + -
89B LYS 3.4 13.9 + - - +
90B ARG 3.2 8.1 + - - +
92B VAL* 1.3 76.6 - - - +
94B ASN* 1.3 57.4 + - - +
96B ARG* 3.0 6.4 + - - +
97B LEU* 2.8 29.6 + - + +
148B ALA* 3.7 21.5 - - + +
153B THR* 3.8 23.1 - - + +
154B ILE* 4.0 11.0 - - + -
155B ALA* 3.8 16.2 - - + -
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Residues in contact with ASN 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ALA* 4.1 15.2 + - + -
70A ILE* 4.0 30.3 - - + +
98A TYR* 5.1 0.9 + - - -
70B ILE* 3.8 11.4 - - - +
83B TYR* 2.6 27.8 + - - -
90B ARG* 2.8 41.8 + - - +
91B ALA* 3.7 6.8 - - - +
93B VAL* 1.3 76.6 - - - +
95B GLN* 1.3 55.7 + - - +
97B LEU* 3.0 8.2 + - - +
98B TYR* 2.9 40.8 + - + -
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Residues in contact with GLN 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLN* 4.1 2.8 + - - -
62A LEU* 3.9 11.2 - - + -
63A TRP* 3.0 61.4 - - + +
64A GLU* 3.7 11.3 - - + +
67A ALA* 3.7 8.6 - - + +
91B ALA 2.8 20.6 + - - +
92B VAL* 3.7 4.4 - - - +
94B ASN* 1.3 74.1 - - - +
96B ARG* 1.3 94.8 + - - +
98B TYR 3.5 0.2 + - - -
99B PHE* 2.9 39.1 + - - +
140B PHE* 4.4 3.4 - - - -
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Residues in contact with ARG 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A TRP* 4.5 9.3 - - - -
92B VAL* 2.9 29.4 + - - +
93B VAL* 3.0 9.8 + - - +
95B GLN* 1.3 110.0 + - - +
97B LEU* 1.3 60.6 + - - +
99B PHE* 3.4 8.5 + - + +
100B ASP* 3.0 26.9 + - - +
137B LEU* 6.1 0.2 - - - +
140B PHE* 3.2 57.4 + - + +
144B GLN* 5.8 1.2 - - - +
147B ALA* 2.8 45.9 + - + +
148B ALA* 4.5 1.1 - - + +
155B ALA* 3.7 14.8 - - + -
159B LEU* 4.3 11.0 - - + +
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A TYR* 3.2 21.3 - - - +
66B ARG* 3.2 20.2 + - + +
69B GLN* 4.3 9.2 - - - +
70B ILE* 4.0 9.4 - - + -
83B TYR* 4.6 0.2 - - + -
93B VAL* 2.8 22.4 + - + +
94B ASN* 3.0 22.0 + - - +
96B ARG* 1.3 73.5 - - - +
98B TYR* 1.3 66.3 + - - +
100B ASP* 3.2 4.1 + - - +
101B MET 3.1 17.0 + - - -
154B ILE* 3.8 31.9 - - + +
155B ALA* 3.6 26.7 - - - +
158B SER* 3.9 15.3 - - - +
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Residues in contact with TYR 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLU* 3.5 28.4 - - + +
66A ARG* 3.4 35.8 - - + +
67A ALA* 4.1 17.5 - - + -
70A ILE* 4.6 9.8 - - + +
94A ASN* 4.6 0.9 + - - -
97A LEU* 3.2 31.9 - - - +
98A TYR* 3.3 49.1 - + - -
101A MET* 3.3 29.3 - - + +
94B ASN* 2.9 31.1 + - + +
97B LEU* 1.3 73.3 - - - +
99B PHE* 1.3 60.4 + - - +
101B MET 3.3 0.2 + - - -
102B GLY* 2.8 28.4 + - - -
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Residues in contact with PHE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLN* 3.7 13.9 - - - -
64A GLU* 4.2 8.7 + - - +
95B GLN* 2.9 28.4 + - - +
96B ARG* 3.5 8.3 - - - +
97B LEU 3.2 0.2 - - - -
98B TYR* 1.3 75.5 - - - +
100B ASP* 1.3 61.1 + - - +
103B THR* 2.8 59.6 + - + -
104B LEU* 3.2 23.5 + - + -
133B ALA 3.5 23.8 - - - -
136B PHE* 3.8 11.4 - - + -
137B LEU* 4.0 16.4 - - + -
140B PHE* 3.6 34.8 - + - -
159B LEU* 4.1 16.8 - - + -
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Residues in contact with ASP 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ARG* 2.5 18.8 + - - -
96B ARG 3.0 14.1 + - - +
97B LEU* 3.2 11.4 + - - +
99B PHE* 1.3 78.3 - - - +
101B MET* 1.3 58.2 + - - +
104B LEU* 3.8 4.1 - - - +
105B TYR* 2.8 34.5 + - - +
158B SER* 2.4 31.0 + - - +
159B LEU* 3.5 28.7 - - + +
162B THR* 2.7 33.2 + - - +
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Residues in contact with MET 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A TYR* 3.4 32.3 - - + +
101A MET* 3.2 29.8 - - + -
102A GLY* 3.3 33.0 - - - +
64B GLU* 3.9 4.5 - - - +
66B ARG* 3.4 30.5 - - - +
97B LEU 3.1 5.8 + - - +
98B TYR* 3.9 4.9 - - - +
100B ASP* 1.3 80.3 - - - +
102B GLY* 1.3 59.1 + - - +
105B TYR* 4.3 6.1 - - + +
106B GLN* 3.1 30.8 + - - +
302B GTX 3.4 27.1 - - - +
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Residues in contact with GLY 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLU* 5.8 0.9 - - - -
101A MET* 3.3 19.4 - - - +
102A GLY* 6.5 0.2 - - - -
106A GLN* 5.1 5.9 - - - +
301A GTX 5.8 1.8 - - - -
98B TYR 2.8 16.2 + - - -
101B MET* 1.3 75.0 - - - +
103B THR* 1.3 61.1 + - - +
106B GLN* 3.3 20.0 - - - +
107B ARG* 5.1 2.6 + - - +
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Residues in contact with THR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLN* 3.2 23.1 + - - +
64A GLU* 4.7 3.6 + - - -
99B PHE* 2.8 45.2 + - + -
101B MET 3.4 0.8 - - - -
102B GLY* 1.3 78.2 + - - +
104B LEU* 1.3 65.8 + - - +
105B TYR 3.6 0.4 - - - -
106B GLN* 4.4 0.2 - - - -
107B ARG* 3.0 53.0 + - - +
133B ALA* 3.9 17.4 - - + +
136B PHE* 4.4 3.1 - - + -
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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