Contacts of the strand formed by residues 63 - 70 (chain A) in PDB entry 3PII
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 GLY 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ILE* 4.0 15.9 - - - -
34A ALA 3.5 9.6 - - - -
35A CYS* 3.7 14.5 - - - -
60A GLY 4.5 1.2 + - - -
61A HIS* 3.6 2.8 - - - +
62A GLU* 1.3 78.5 - - - +
64A VAL* 1.3 56.8 + - - +
84A GLY* 3.5 1.0 - - - -
85A ILE* 2.8 40.2 + - - +
119A GLY* 4.3 5.4 - - - -
147A PHE* 5.2 0.2 - - - -
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Residues in contact with VAL 64 (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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30A VAL* 5.6 0.7 - - - -
32A ILE* 3.8 5.9 - - - +
33A LYS* 3.0 17.8 + - - -
34A ALA* 2.9 31.7 + - + +
62A GLU 3.9 1.8 - - - +
63A GLY* 1.3 76.4 - - - +
65A GLY* 1.3 58.6 + - - +
83A VAL 3.3 4.9 - - - -
84A GLY* 4.0 2.2 - - - -
134A ILE* 3.5 24.5 - - + -
140A PHE* 3.6 39.7 - - + +
144A ALA* 3.9 19.3 - - + +
147A PHE* 3.8 22.7 - - + -
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Residues in contact with GLY 65 (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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30A VAL* 4.2 9.2 - - - +
31A ARG 3.3 13.2 - - - -
33A LYS* 3.7 7.6 - - - -
64A VAL* 1.3 73.6 - - - +
66A ILE* 1.3 63.5 + - - -
82A ARG* 3.5 1.7 - - - -
83A VAL* 2.9 32.2 + - - -
140A PHE* 3.2 17.8 - - - -
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Residues in contact with ILE 66 (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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30A VAL* 3.2 6.2 - - - +
31A ARG* 2.8 53.9 + - - +
33A LYS* 4.2 24.0 - - + -
65A GLY* 1.3 75.3 - - - +
67A VAL* 1.3 69.3 + - - +
68A GLU* 2.8 11.7 + - - +
80A GLY* 3.7 27.4 - - - +
81A ASP 3.5 2.9 - - - +
82A ARG* 3.8 14.8 - - + -
83A VAL* 5.5 0.2 - - - -
140A PHE* 3.6 26.7 - - + -
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Residues in contact with VAL 67 (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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28A VAL* 3.9 25.8 - - + -
29A LEU 3.7 5.4 - - - +
30A VAL* 4.6 5.6 - - + +
66A ILE* 1.3 70.5 - - - +
68A GLU* 1.3 58.0 + - - +
69A GLU 4.0 7.6 - - - +
70A VAL* 3.9 18.6 - - + -
77A LEU* 4.7 11.9 - - + -
78A LYS 3.9 13.2 - - - +
79A VAL* 3.4 8.4 - - - +
80A GLY* 2.6 27.7 + - - -
81A ASP* 3.0 22.0 + - + +
83A VAL* 3.9 30.7 - - + -
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Residues in contact with GLU 68 (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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20A LYS* 3.9 8.0 + - - -
29A LEU* 2.9 16.7 + - + +
31A ARG* 2.8 38.9 + - - +
66A ILE* 2.8 11.7 + - - +
67A VAL* 1.3 73.4 - - - +
69A GLU* 1.3 63.4 + - + +
79A VAL* 3.1 17.0 - - - +
123A TYR* 2.6 41.7 + - + -
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Residues in contact with GLU 69 (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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20A LYS* 5.6 2.6 + - - -
22A THR* 5.8 1.0 + - - -
23A ILE* 3.4 33.2 + - + +
28A VAL* 3.6 5.5 - - - +
29A LEU* 3.1 49.5 + - + +
67A VAL* 4.0 2.6 - - - +
68A GLU* 1.3 82.7 - - - +
70A VAL* 1.3 64.4 + - - +
79A VAL* 4.4 4.3 - - + -
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Residues in contact with VAL 70 (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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23A ILE* 3.9 2.0 - - - +
28A VAL* 4.0 6.7 - - + -
67A VAL* 3.9 22.4 - - + -
69A GLU* 1.3 75.6 - - - +
71A GLY* 1.3 63.6 + - - +
72A PRO* 4.5 0.9 - - - +
74A VAL* 3.4 27.1 - - + +
77A LEU 3.6 17.7 - - - +
78A LYS* 5.6 0.2 - - - -
79A VAL* 4.2 24.6 - - + +
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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