Contacts of the strand formed by residues 77 - 83 (chain A) in PDB entry 2PMI
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 LYS 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLU* 5.7 7.6 - - + +
38A VAL 5.4 0.2 - - - -
39A LYS* 3.9 13.9 - - + +
40A LEU* 3.9 3.7 - - - +
72A ILE 3.5 0.7 - - - +
74A THR* 2.8 48.7 + - + +
75A GLU* 3.3 7.0 + - + +
76A ASN* 1.3 88.0 - - + +
78A LEU* 1.3 60.8 + - - +
79A THR* 5.0 6.3 - - + -
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Residues in contact with LEU 78 (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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37A GLU* 3.5 1.9 - - - +
38A VAL* 2.6 52.8 + - + +
40A LEU* 3.9 24.0 - - + +
46A THR* 5.0 2.9 - - + -
50A ALA* 4.5 13.7 - - + -
54A ILE* 3.6 29.6 - - + -
71A VAL* 3.7 13.2 - - + -
72A ILE 3.7 1.1 - - - -
73A HIS* 3.6 28.9 - - + -
77A LYS* 1.3 75.0 - - - +
79A THR* 1.3 60.0 + - - +
80A LEU* 3.9 9.1 + - + -
160B ASN* 5.3 0.2 - - - +
168B TYR* 3.3 24.9 - - + +
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Residues in contact with THR 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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35A LEU* 4.8 11.5 - - + +
36A LYS 3.2 9.2 - - - -
37A GLU* 3.9 27.4 - - + +
70A ASP 4.0 0.2 - - - +
71A VAL* 3.5 3.5 - - - -
72A ILE* 2.8 61.3 + - + +
74A THR* 5.6 2.0 - - + -
77A LYS* 5.0 7.2 - - + -
78A LEU* 1.3 82.0 - - - +
80A LEU* 1.3 64.8 + - - +
81A VAL* 3.9 4.7 + - - +
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Residues in contact with LEU 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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34A ALA 3.5 2.6 - - - +
35A LEU* 3.8 1.2 - - - -
36A LYS* 2.9 42.7 + - + +
38A VAL* 4.9 8.5 - - + -
50A ALA* 5.0 5.8 - - + +
53A GLU* 3.6 28.5 - - + +
54A ILE* 3.6 40.4 - - + +
68A LEU* 3.7 9.9 - - + -
70A ASP 3.8 4.3 - - - -
71A VAL* 4.6 3.1 - - + +
78A LEU* 3.9 17.9 - - + +
79A THR* 1.3 79.1 - - - +
81A VAL* 1.3 60.3 + - - +
82A PHE* 3.5 29.1 + - + -
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Residues in contact with VAL 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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33A VAL* 3.5 40.8 - - + -
34A ALA 3.5 2.5 - - - -
35A LEU* 3.5 19.5 - - + -
68A LEU* 3.7 3.3 - - - +
69A TYR* 2.7 41.5 + - + +
70A ASP* 2.8 30.8 + - + +
72A ILE* 4.3 18.4 - - + -
79A THR* 4.3 7.0 - - - +
80A LEU* 1.3 70.3 - - - +
82A PHE* 1.3 52.6 + - - +
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Residues in contact with PHE 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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33A VAL* 3.5 5.9 - - - +
34A ALA* 2.8 43.3 + - + +
36A LYS* 3.9 28.3 - - + -
53A GLU* 3.9 19.5 - - + -
57A MET* 4.4 22.4 - - + -
66A VAL* 4.0 23.3 - - + -
67A ARG 3.5 6.3 - - - -
68A LEU* 3.6 18.2 - - + -
69A TYR* 4.1 2.0 - - - -
80A LEU* 3.5 43.7 - - + -
81A VAL* 1.3 73.6 - - - +
83A GLU* 1.3 65.4 + - - +
84A PHE 3.1 0.2 + - - -
3001A AGS 4.4 8.7 - - - +
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Residues in contact with GLU 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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66A VAL* 3.4 14.7 - - + +
67A ARG* 2.7 47.9 + - + +
69A TYR* 3.4 34.6 + - + +
82A PHE* 1.3 72.0 - - - +
84A PHE* 1.3 64.2 + - - +
85A MET* 3.3 17.9 + - + +
142A ASN* 5.2 1.6 + - - -
148A LYS* 2.6 41.7 + - - +
3001A AGS 3.4 10.6 + - - -
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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