Contacts of the helix formed by residues 64 - 76 (chain B) in PDB entry 2PDA
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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28B TYR* 3.2 29.1 - - + +
30B ILE* 4.0 11.1 - - - +
63B SER* 1.3 71.5 - - - +
65B ALA* 1.3 60.7 + - - +
67B ALA* 3.6 9.2 - - - -
68B ALA 2.9 17.3 + - - -
85B THR* 4.2 2.5 + - - +
89B GLY* 3.2 38.3 - - - +
92B LEU* 4.0 8.0 - - + +
93B MET* 3.0 31.6 - - + +
969B ILE* 3.8 2.8 - - - +
1243B TPP 2.5 40.3 + - - +
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A GLU* 6.3 3.4 - - + -
871A ASP* 5.0 2.6 - - - +
874A GLU* 4.9 1.1 - - - +
62B GLN* 6.0 0.2 - - - +
63B SER* 3.1 9.3 + - - +
64B GLU* 1.3 77.5 - - - +
66B GLY* 1.3 66.7 + - - +
68B ALA* 3.0 5.0 + - - +
69B GLY* 2.9 20.1 + - - -
92B LEU* 3.7 34.8 - - + +
96B ASN* 3.8 5.9 + - - +
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Residues in contact with GLY 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874A GLU* 3.6 25.7 - - - +
61B MET* 3.8 6.7 - - - -
62B GLN* 3.6 18.8 - - - +
63B SER* 3.1 11.1 + - - -
65B ALA* 1.3 79.0 - - - +
67B ALA* 1.3 56.3 + - - +
69B GLY* 3.0 3.3 + - - -
70B ALA* 2.9 27.7 + - - +
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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
----------------------------------------------------------
26B ALA* 3.7 18.8 - - - +
27B ILE* 4.0 19.5 - - - +
61B MET* 3.5 12.9 - - + +
63B SER 2.9 13.5 + - - +
64B GLU* 3.8 14.1 - - + +
66B GLY* 1.3 76.8 - - - +
68B ALA* 1.3 55.7 + - - +
71B VAL* 2.9 35.2 + - - +
93B MET* 3.8 12.3 - - + -
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLU 2.9 16.1 + - - +
65B ALA* 3.0 10.0 + - - +
67B ALA* 1.3 76.6 - - - +
69B GLY* 1.3 58.2 + - - +
71B VAL* 3.3 7.2 + - - +
72B HIS* 3.0 26.3 + - - +
93B MET* 3.3 32.7 - - + +
96B ASN* 3.3 24.2 - - + +
100B ILE* 4.2 2.3 - - - +
109B PHE* 5.2 4.5 - - + -
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Residues in contact with GLY 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867A SER* 5.1 0.7 - - - -
871A ASP* 3.7 15.5 - - - -
874A GLU* 3.9 5.8 - - - -
875A TYR* 3.5 11.8 - - - -
65B ALA 2.9 12.6 + - - -
66B GLY 3.0 3.6 + - - -
68B ALA* 1.3 75.4 - - - +
70B ALA* 1.3 58.5 + - - +
72B HIS* 3.2 2.9 + - - +
73B GLY 3.0 23.7 + - - -
96B ASN* 3.3 19.4 - - - +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874A GLU 3.3 18.1 + - - +
877A PHE* 4.7 4.5 - - + -
878A GLY* 3.3 13.1 - - - -
881A MET* 4.9 2.4 - - - +
24B VAL* 6.3 0.2 - - - -
26B ALA* 3.4 24.9 - - + -
61B MET* 4.3 13.7 - - + -
66B GLY 2.9 14.6 + - - +
67B ALA* 4.2 1.6 - - - -
69B GLY* 1.3 73.3 - - - +
71B VAL* 1.3 66.7 + - - +
72B HIS 3.2 0.2 + - - -
73B GLY 3.3 1.0 + - - -
74B ALA* 3.1 23.3 + - - +
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA* 3.8 10.1 - - + +
67B ALA 2.9 21.4 + - - +
68B ALA* 3.5 7.2 - - - +
70B ALA* 1.3 77.0 - - - +
72B HIS* 1.3 61.0 + - - +
74B ALA* 3.6 1.9 + - - +
75B LEU* 3.3 36.1 + - + +
81B THR* 3.8 23.7 + - + +
82B THR 3.6 22.2 - - - +
83B THR* 3.8 15.3 - - + -
100B ILE* 4.6 3.1 - - + -
107B GLY* 5.5 0.2 - - - -
109B PHE* 3.8 25.8 - - + -
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Residues in contact with HIS 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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866A ASN 4.8 0.7 - - - -
867A SER* 2.9 33.9 + - - -
875A TYR* 3.5 17.7 + + - -
68B ALA 3.0 14.1 + - - +
69B GLY 3.5 7.6 - - - +
70B ALA 3.1 0.2 - - - -
71B VAL* 1.3 78.6 - - - +
73B GLY* 1.3 63.7 + - - +
74B ALA 3.3 0.2 + - - -
75B LEU* 3.4 3.0 + - - +
76B ALA* 3.0 21.5 + - + +
96B ASN* 3.7 11.9 + - - +
99B LYS* 3.8 19.3 - - + +
100B ILE* 3.9 23.8 - - + -
103B GLU* 3.1 28.9 + - - -
105B LEU* 3.9 17.2 - - + +
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Residues in contact with GLY 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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875A TYR* 3.2 39.1 - - - -
879A MET* 3.4 16.1 - - - +
69B GLY 3.0 11.9 + - - -
70B ALA 3.3 0.8 + - - -
72B HIS* 1.3 75.7 - - - +
74B ALA* 1.3 56.9 + - - +
76B ALA* 3.5 1.3 - - - +
77B ALA* 2.9 28.9 + - - +
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Residues in contact with ALA 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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878A GLY* 3.4 19.6 - - - +
882A SER* 3.6 7.5 - - - -
24B VAL* 4.0 18.2 - - + -
70B ALA 3.1 16.6 + - - +
71B VAL 3.8 2.2 - - - +
72B HIS 3.2 0.2 - - - -
73B GLY* 1.3 75.5 - - - +
75B LEU* 1.3 58.9 + - - +
77B ALA* 2.9 19.4 + - - +
79B ALA* 3.2 18.7 + - + -
81B THR* 3.3 19.7 - - + +
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Residues in contact with LEU 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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71B VAL* 3.3 27.2 + - + +
72B HIS* 3.8 1.1 - - - +
74B ALA* 1.3 74.5 - - - +
76B ALA* 1.3 70.0 + - - +
78B GLY 3.0 9.2 + - - -
79B ALA 3.4 18.3 + - - +
80B LEU* 4.2 0.4 - - - -
81B THR* 3.8 20.9 - - - +
100B ILE* 4.1 12.6 - - + -
105B LEU* 3.7 27.9 - - + +
106B PRO* 4.0 22.0 - - + -
107B GLY* 3.5 25.6 - - - +
203B PHE* 3.5 28.0 - - + -
207B SER* 3.7 0.5 + - - -
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A TYR* 4.1 14.1 - - + +
72B HIS* 3.0 18.1 + - + +
73B GLY* 3.5 7.2 - - - +
75B LEU* 1.3 79.8 - - - +
77B ALA* 1.3 57.8 + - - +
78B GLY 2.9 7.6 + - - -
105B LEU* 4.0 2.8 - - - +
207B SER* 3.1 11.4 + - - -
208B MET* 3.2 36.8 + - - +
216B ARG* 4.2 23.9 + - - +
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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