Contacts of the helix formed by residues 64 - 77 (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 GLU 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLN* 3.7 29.6 - - + +
98A TYR* 3.6 27.8 - - + +
99A PHE* 4.0 12.8 - - - -
102A GLY* 5.8 0.5 - - - -
103A THR* 4.4 8.3 + - - -
49B GLN* 4.5 9.7 + - - +
51B CYS* 5.3 1.4 - - - -
53B PRO 3.9 2.4 + - - -
63B TRP* 1.3 96.0 - - + +
65B SER* 1.3 66.6 + - - +
66B ARG 3.3 2.4 + - - -
67B ALA* 3.0 21.4 + - + +
68B ILE* 3.0 8.2 + - - +
101B MET* 3.9 2.4 - - - +
302B GTX 2.8 43.9 + - - +
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Residues in contact with SER 65 (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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11B PRO* 3.4 38.4 - - - +
14B ALA* 4.9 1.0 - - - +
15B VAL* 3.8 5.4 - - - +
53B PRO* 3.7 14.1 - - - +
64B GLU* 1.3 70.9 - - - +
66B ARG* 1.3 75.8 + - - +
68B ILE* 3.0 6.8 + - - +
69B GLN* 2.8 35.7 + - - +
302B GTX 2.7 30.9 + - - -
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Residues in contact with ARG 66 (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* 3.5 33.0 - - + +
11B PRO* 5.3 8.1 - - - +
64B GLU* 3.3 1.2 + - - -
65B SER* 1.3 82.2 + - - +
67B ALA* 1.3 64.2 + - - +
69B GLN* 3.5 23.4 - - - +
70B ILE* 3.2 29.1 + - - +
97B LEU* 3.2 35.3 + - + +
100B ASP* 2.5 34.3 + - - -
101B MET* 3.4 34.2 - - - +
105B TYR* 4.3 13.3 - - - +
158B SER* 3.2 6.3 + - - +
162B THR* 4.4 1.6 + - - -
302B GTX 3.0 28.3 + - - -
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Residues in contact with ALA 67 (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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91A ALA* 4.1 8.0 - - - +
94A ASN* 3.9 15.9 - - + +
95A GLN* 3.6 32.3 - - + +
98A TYR* 4.0 5.2 - - + -
62B LEU* 4.1 4.3 - - + +
63B TRP 3.8 10.5 - - - +
64B GLU* 3.0 13.2 + - + +
66B ARG* 1.3 75.5 - - - +
68B ILE* 1.3 60.5 + - - +
70B ILE* 3.4 3.5 + - - +
71B TYR* 2.9 29.5 + - - +
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Residues in contact with ILE 68 (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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3B PHE* 5.3 0.4 - - + -
15B VAL* 3.6 29.4 - - + -
53B PRO* 3.8 37.9 - - + +
55B LEU* 4.0 28.7 - - + +
62B LEU* 3.6 42.2 - - + +
63B TRP* 4.0 1.1 - - - -
64B GLU 3.0 13.6 + - - +
65B SER 3.0 5.8 + - - +
67B ALA* 1.3 78.3 - - - +
69B GLN* 1.3 63.0 + - - +
71B TYR* 3.2 1.9 + - - +
72B LEU* 2.9 26.5 + - + +
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Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ALA* 3.9 22.7 - - - +
15B VAL* 4.5 3.4 - - - -
18B THR* 3.0 40.0 + - + +
65B SER 2.8 14.1 + - - +
66B ARG* 3.5 30.2 - - - +
68B ILE* 1.3 78.0 - - - +
70B ILE* 1.3 62.9 + - - +
72B LEU* 3.3 3.5 + - - +
73B ALA* 3.0 23.4 + - - +
97B LEU* 4.3 3.1 - - + +
154B ILE* 3.0 36.9 - - + +
157B LEU* 4.0 0.3 - - - +
158B SER* 3.5 27.6 + - - -
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Residues in contact with ILE 70 (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* 6.1 1.1 - - + -
83A TYR* 5.5 0.7 - - - +
90A ARG* 5.2 0.4 - - - -
94A ASN* 3.7 33.0 - - - +
98A TYR* 4.5 8.7 - - + +
66B ARG 3.2 18.0 + - - +
67B ALA 3.8 3.6 - - - +
68B ILE 3.3 0.2 - - - -
69B GLN* 1.3 75.0 - - - +
71B TYR* 1.3 64.9 + - - +
73B ALA* 3.2 2.8 + - - +
74B GLU* 3.0 39.4 + - - +
83B TYR* 3.3 37.9 - - + +
94B ASN* 3.8 9.9 - - - +
97B LEU* 4.0 9.6 - - + -
154B ILE* 3.7 22.4 - - + -
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Residues in contact with TYR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PRO* 3.7 20.2 - - + -
88A GLN* 4.0 19.4 + - - -
91A ALA* 3.8 11.4 - - + +
55B LEU* 4.2 16.2 - - + -
57B ASP* 2.6 41.6 + - + +
60B PHE* 4.1 17.1 - + - +
62B LEU* 3.8 20.9 - - + -
67B ALA 2.9 18.9 + - - +
68B ILE 3.2 4.0 + - - +
70B ILE* 1.3 77.0 - - - +
72B LEU* 1.3 62.3 + - + +
74B GLU* 4.3 5.5 - - - +
75B LYS* 2.9 72.2 + - + +
76B TYR* 4.4 6.1 - + - -
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Residues in contact with LEU 72 (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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1B MET* 4.3 8.3 - - - -
15B VAL* 3.9 28.5 - - + +
18B THR* 4.3 10.8 - - + -
19B ALA* 4.2 27.4 - - + +
22B VAL* 3.7 10.2 - - + +
24B VAL* 5.0 7.4 - - + -
26B LEU* 5.0 4.9 - - + -
55B LEU* 4.2 19.3 - - + -
68B ILE* 2.9 23.9 + - + +
69B GLN 3.7 3.6 - - - +
71B TYR* 1.3 81.8 - - + +
73B ALA* 1.3 57.1 + - - +
76B TYR* 2.9 52.2 + - + +
77B GLY 3.2 4.5 + - - -
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Residues in contact with ALA 73 (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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18B THR* 4.8 0.4 - - + +
22B VAL* 4.0 14.5 - - + +
69B GLN 3.0 16.5 + - - +
70B ILE* 3.7 6.1 - - - +
72B LEU* 1.3 76.7 - - - +
74B GLU* 1.3 58.5 + - - +
77B GLY* 2.8 29.6 + - - +
80B ASP* 5.1 6.8 - - - +
82B LEU* 5.0 4.9 - - + -
83B TYR* 3.9 28.3 - - + -
154B ILE* 4.4 13.0 - - + -
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Residues in contact with GLU 74 (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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85A LYS 5.0 2.3 - - - +
87A PRO* 4.3 26.0 - - + +
90A ARG* 3.4 33.7 + - - +
70B ILE* 3.0 31.3 + - + +
71B TYR* 4.3 2.9 - - - +
73B ALA* 1.3 76.6 - - - +
75B LYS* 1.3 63.0 + - - +
77B GLY 4.5 5.2 + - - +
80B ASP* 5.6 4.3 - - - +
83B TYR* 3.6 16.2 - - + -
90B ARG* 3.2 27.4 + - - +
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Residues in contact with LYS 75 (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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87A PRO* 4.0 21.3 - - + +
88A GLN* 4.8 13.5 + - - +
57B ASP* 4.4 2.8 + - - -
71B TYR* 2.9 58.6 + - + +
74B GLU* 1.3 80.5 - - - +
76B TYR* 1.3 91.4 + - + +
77B GLY 5.2 0.2 - - - -
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Residues in contact with TYR 76 (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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1B MET* 3.4 23.3 - - + +
22B VAL* 3.1 29.3 - - + +
24B VAL* 3.5 20.9 - - + -
57B ASP* 2.6 36.6 + - - -
71B TYR* 4.4 1.6 - + - -
72B LEU* 2.9 25.5 + - + +
75B LYS* 1.3 108.1 - - + +
77B GLY* 1.3 65.6 + - - +
78B LYS* 3.7 4.0 + - - +
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Residues in contact with GLY 77 (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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22B VAL* 3.3 17.2 - - - +
72B LEU 3.2 3.2 + - - -
73B ALA* 2.8 25.0 + - - +
74B GLU 4.6 4.9 - - - +
75B LYS 3.7 0.5 - - - +
76B TYR* 1.3 79.8 - - - +
78B LYS* 1.3 59.7 + - - -
79B ASP 4.3 0.5 + - - -
80B ASP* 4.7 10.1 + - - +
82B LEU* 6.2 0.4 - - - -
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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