Contacts of the helix formed by residues 62 - 70 (chain B) in PDB entry 2PWY
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 THR 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A THR 5.5 1.3 - - - -
88A LEU 5.4 1.8 - - - +
90A ASP* 3.4 28.5 - - + +
189A ARG* 4.7 2.9 - - - +
190A PHE* 3.5 35.2 - - + -
250A ARG* 5.4 1.1 - - - +
60B ARG 3.5 2.4 + - - +
61B PRO* 1.3 74.7 - - - +
63B LEU* 1.3 59.7 + - - +
64B GLU* 3.5 11.3 + - - +
65B GLU* 2.8 42.4 + - - +
66B TYR* 2.8 27.9 + - - +
141B PHE* 4.0 1.6 - - - -
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Residues in contact with LEU 63 (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 THR* 6.2 0.7 - - + -
90A ASP* 2.9 18.9 + - - +
62B THR* 1.3 71.7 - - - +
64B GLU* 1.3 63.5 + - - +
66B TYR* 3.3 2.0 + - + -
67B LEU* 2.9 34.7 + - + +
109B LEU* 3.6 28.7 - - + -
110B PHE* 3.6 48.7 - - + +
113B ARG* 3.7 36.8 - - - +
141B PHE* 3.6 23.9 - - + -
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Residues in contact with GLU 64 (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 THR* 4.6 17.5 + - + +
88A LEU* 4.0 8.3 - - - +
217A ARG* 2.9 45.2 + - - -
62B THR* 3.2 10.3 + - - +
63B LEU* 1.3 78.2 - - - +
65B GLU* 1.3 63.5 - - + +
67B LEU* 3.5 2.1 + - - +
68B LEU* 3.2 40.6 + - + +
79B PRO* 3.6 28.9 - - + +
110B PHE* 4.7 3.6 - - - -
223B TRP* 3.8 15.4 - - - -
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Residues in contact with GLU 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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190A PHE* 4.9 1.0 - - - -
250A ARG* 3.2 26.2 + - - -
8B LEU* 3.4 31.5 - - + +
10B LYS* 3.8 8.4 - - - -
59B HIS* 5.2 1.0 - - - +
60B ARG 4.2 1.9 - - - +
61B PRO* 3.3 11.4 - - + +
62B THR* 2.8 46.7 + - - +
64B GLU* 1.3 79.4 - - + +
66B TYR* 1.3 62.7 + - - +
68B LEU* 3.3 5.3 + - + -
69B HIS* 2.8 37.3 + - + +
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Residues in contact with TYR 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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6B PRO* 3.8 19.5 - - + -
18B LEU* 3.7 35.4 - - + -
20B PHE* 4.2 6.7 - + - -
61B PRO* 4.2 6.1 - - + +
62B THR 2.8 19.5 + - - +
63B LEU* 3.6 4.7 - - + +
65B GLU* 1.3 72.5 - - - +
67B LEU* 1.3 64.0 + - - +
69B HIS 3.1 0.9 + - - -
70B MET* 2.8 53.1 + - + +
109B LEU* 3.7 19.5 - - + -
137B ASN* 2.6 40.1 + - - +
140B ALA* 3.5 12.6 - - - +
141B PHE* 3.5 37.9 - + + -
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Residues in contact with LEU 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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63B LEU* 2.9 41.1 + - + +
64B GLU 3.8 4.5 - - - +
66B TYR* 1.3 72.4 - - - +
68B LEU* 1.3 62.4 + - - +
69B HIS 3.3 0.3 + - - -
70B MET* 3.6 19.2 + - + +
72B ARG* 4.4 2.1 + - - -
76B PRO* 3.7 20.2 - - + +
77B THR 3.2 26.5 - - - +
78B TYR 4.8 0.2 - - - -
79B PRO* 4.3 13.0 - - + -
82B ALA* 4.9 1.6 - - + -
106B GLY* 3.4 44.0 - - - +
107B LEU 4.4 0.2 - - - +
109B LEU* 4.2 8.3 - - + -
110B PHE* 3.6 22.2 - - + -
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Residues in contact with LEU 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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64B GLU* 3.2 38.7 + - + +
65B GLU* 3.8 7.9 - - + +
66B TYR 3.2 1.4 - - - -
67B LEU* 1.3 79.7 - - - +
69B HIS* 1.3 73.6 + - + +
72B ARG* 3.2 27.5 + - - +
76B PRO* 5.7 0.2 - - - -
78B TYR* 4.3 19.5 - - + -
79B PRO* 3.8 24.2 - - + -
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Residues in contact with HIS 69 (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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8B LEU* 4.0 14.8 - - + +
16B ALA* 3.4 43.8 + - + +
17B TYR* 5.5 0.2 - - - -
18B LEU* 3.9 28.9 + - + +
65B GLU* 2.8 34.3 + - + +
66B TYR 3.1 2.6 + - - +
68B LEU* 1.3 95.0 + - + +
70B MET* 1.3 66.3 + - - +
71B LYS* 3.7 0.7 + - - -
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Residues in contact with MET 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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18B LEU* 3.7 11.6 - - + +
20B PHE* 5.9 1.6 - - + -
66B TYR* 2.8 54.9 + - + +
67B LEU* 3.6 14.6 - - + +
69B HIS* 1.3 81.8 - - - +
71B LYS* 1.3 69.8 + - - +
72B ARG* 3.4 17.5 + - + +
76B PRO* 4.1 12.6 - - + -
104B SER* 3.4 31.0 - - - +
105B GLY 4.2 0.2 - - - -
106B GLY* 3.6 24.9 - - - +
109B LEU* 4.7 2.0 - - - -
137B ASN* 3.8 18.4 - - - +
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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