Contacts of the helix formed by residues 78 - 91 (chain A) in PDB entry 2PGW
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
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Residue Dist Surf HB Arom Phob DC
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74A HIS* 5.7 1.0 - - + +
75A SER* 2.9 29.5 + - - +
77A HIS* 1.3 85.4 - - - +
79A VAL* 1.3 63.3 + - - +
80A ALA 3.4 2.2 - - - -
81A PRO* 3.3 11.3 - - + +
82A LEU* 3.1 35.8 + - + +
127B GLN* 3.9 18.0 + - - +
130B GLY 3.4 4.5 - - - -
131B GLY* 4.0 8.5 - - - -
132B ALA* 4.5 4.0 + - - -
352B ARG* 5.5 4.1 + - - -
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Residues in contact with VAL 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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76A PRO 3.7 10.0 + - - +
77A HIS 4.8 0.2 - - - +
78A ASP* 1.3 76.2 - - - +
80A ALA* 1.3 70.0 + - - +
82A LEU* 3.7 1.4 - - - +
83A ILE* 3.0 37.7 + - + +
110A ASP* 3.2 25.1 - - - +
113A MSE 3.8 35.0 - - + +
114A TRP* 3.8 20.0 - - + +
117A GLN* 3.7 20.9 - - - +
279A GLN* 4.0 3.6 - - - +
130B GLY* 3.3 8.9 + - - +
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Residues in contact with ALA 80 (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 VAL* 1.3 77.0 - - - +
81A PRO* 1.3 69.3 - - + +
83A ILE* 3.9 4.0 - - - +
84A ALA* 3.1 21.8 + - - +
279A GLN* 3.7 22.2 - - - +
129B LEU 5.2 0.4 - - - +
130B GLY* 2.9 20.8 + - - +
133B HIS* 3.7 20.1 - - + +
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Residues in contact with PRO 81 (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* 3.3 20.2 - - + +
80A ALA* 1.3 93.5 - - + +
82A LEU* 1.3 55.8 + - + +
84A ALA* 3.7 4.2 - - + +
85A ARG* 2.9 31.0 + - - +
130B GLY 3.3 13.2 - - - +
131B GLY 3.9 11.4 - - - +
132B ALA 3.2 26.5 - - - +
133B HIS* 3.6 23.1 - - + +
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Residues in contact with LEU 82 (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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6A ILE* 5.3 0.4 - - + -
70A HIS 4.8 0.4 - - - +
71A LEU* 4.0 20.4 - - + -
74A HIS* 3.9 40.4 - - + +
75A SER 3.6 21.8 - - - +
78A ASP* 3.1 34.4 + - + +
79A VAL* 3.7 4.3 - - - +
81A PRO* 1.3 78.5 - - + +
83A ILE* 1.3 58.1 + - - +
85A ARG* 3.3 22.4 + - - +
86A ILE* 2.9 36.7 + - + +
113A MSE 3.8 14.1 - - + -
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Residues in contact with ILE 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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71A LEU* 5.6 1.6 - - + -
79A VAL* 3.0 39.4 + - + +
80A ALA* 3.9 4.5 - - - +
82A LEU* 1.3 76.9 - - + +
84A ALA* 1.3 59.7 + - - +
86A ILE* 3.3 4.9 + - + +
87A PHE* 2.8 30.2 + - + +
106A PHE* 3.5 48.3 - - + +
109A ILE* 4.3 11.9 - - + -
110A ASP* 4.0 28.7 - - + +
113A MSE 6.5 0.2 - - + -
276A GLY 5.2 1.3 - - - +
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Residues in contact with ALA 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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80A ALA 3.1 16.8 + - - +
81A PRO* 3.7 8.1 - - + +
82A LEU 3.3 0.2 - - - -
83A ILE* 1.3 77.5 - - - +
85A ARG* 1.3 58.6 + - - +
87A PHE* 3.3 10.1 + - - +
88A HIS* 2.9 29.5 + - - +
133B HIS* 5.2 7.9 - - + +
318B PRO* 6.4 0.7 - - + -
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Residues in contact with ARG 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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70A HIS* 3.6 39.6 + - - +
74A HIS* 4.1 11.7 + - - -
81A PRO 2.9 17.2 + - - +
82A LEU* 3.6 23.0 - - - +
84A ALA* 1.3 77.1 - - - +
86A ILE* 1.3 64.4 + - - +
88A HIS* 3.2 1.8 + - - -
89A GLN* 2.8 54.0 + - - +
26G TYR* 3.3 33.1 + - + +
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Residues in contact with ILE 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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67A LEU* 3.7 37.0 - - + +
70A HIS* 3.6 44.6 - - + -
71A LEU* 4.0 23.3 - - + -
82A LEU* 2.9 24.8 + - + +
83A ILE* 3.7 7.4 - - + +
85A ARG* 1.3 84.9 - - - +
87A PHE* 1.3 57.6 + - - +
89A GLN* 4.5 4.5 - - - -
90A GLU* 2.8 33.4 + - + +
91A TYR* 4.5 0.2 - - - -
106A PHE* 3.9 11.7 - - + -
109A ILE* 5.7 2.0 - - + -
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Residues in contact with PHE 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 ILE* 2.8 18.4 + - + +
84A ALA* 3.5 8.3 - - - +
86A ILE* 1.3 77.3 - - - +
88A HIS* 1.3 62.9 + - - +
91A TYR* 3.0 54.9 + + + +
92A LEU* 3.2 37.0 + - + -
96A ALA 5.0 0.4 - - - -
98A ILE 4.6 2.9 - - - -
99A MSE 4.0 27.4 - - + -
102A ALA* 3.5 26.7 - - + -
106A PHE* 3.7 15.2 - + + -
228G TRP* 3.7 23.8 - + - -
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Residues in contact with HIS 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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84A ALA 2.9 16.8 + - - +
85A ARG* 4.4 0.7 - - - -
87A PHE* 1.3 77.2 - - - +
89A GLN* 1.3 56.8 + - - +
92A LEU* 3.7 34.1 - - + +
93A GLY* 2.7 35.3 + - - -
25G SER* 3.5 23.5 + - - -
26G TYR* 3.1 38.3 - + - +
198G ASN* 6.2 2.0 - - - -
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Residues in contact with GLN 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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70A HIS* 3.6 25.0 + - - -
85A ARG* 2.8 40.9 + - - +
86A ILE* 3.9 4.0 - - - +
88A HIS* 1.3 79.1 - - - +
90A GLU* 1.3 65.4 + - + +
94A HIS* 3.1 24.4 + - - -
24G TRP* 3.2 21.2 - - + -
26G TYR* 3.4 42.8 - - + +
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Residues in contact with GLU 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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66A ARG* 2.9 47.3 + - - +
67A LEU* 4.4 9.4 - - + -
70A HIS* 2.8 40.0 + - + +
86A ILE* 2.8 23.4 + - + +
89A GLN* 1.3 82.0 - - + +
91A TYR* 1.3 67.7 + - + +
94A HIS* 3.7 12.1 + - - -
24G TRP* 5.9 0.2 - - - -
54G ALA* 3.7 8.7 - - - +
55G PRO* 3.5 30.5 - - + +
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Residues in contact with TYR 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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63A ILE* 3.7 3.3 - - - +
67A LEU* 3.8 21.0 - - + +
87A PHE* 3.0 40.4 + + + +
89A GLN 3.4 0.4 - - - -
90A GLU* 1.3 83.3 - - + +
92A LEU* 1.3 65.7 + - - +
93A GLY 3.3 1.3 - - - -
94A HIS* 2.9 15.1 + - - +
96A ALA* 3.1 32.7 + - + +
98A ILE* 3.7 36.1 - - + -
101A ALA* 5.2 0.7 - - + -
102A ALA* 3.8 19.4 - - + -
105A ILE* 3.2 31.4 - - - +
106A PHE* 4.2 5.8 - + - -
55G PRO* 3.6 35.6 - - + +
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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