Contacts of the strand formed by residues 78 - 84 (chain E) in PDB entry 3P1M
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 78 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A SER* 5.3 2.9 - - - -
185A ALA* 3.4 23.4 + - - +
187A ASN* 2.6 32.2 + - - -
188D LEU* 6.0 0.9 - - + -
189D TYR 3.2 13.8 + - - +
190D PHE* 4.8 10.8 - - + -
191D GLN* 4.9 10.2 - - + +
70E HIS* 4.3 21.1 - - + -
71E PHE 3.3 12.6 - - - +
72E ILE* 4.3 7.4 - - + +
77E GLU* 1.3 77.3 - - - +
79E LEU* 1.3 68.3 + - - +
80E THR* 4.2 6.1 + - - +
164E THR* 5.6 0.2 - - + -
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Residues in contact with LEU 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E VAL 3.8 1.0 - - - +
70E HIS* 3.5 1.8 - - - -
71E PHE* 2.8 49.4 + - + +
73E ASN* 4.0 23.1 - - + +
77E GLU* 4.2 21.8 - - + +
78E THR* 1.3 79.0 - - - +
80E THR* 1.3 62.0 + - - +
81E THR* 4.1 0.4 + - - -
98E LEU* 4.1 29.8 - - + -
99E ASP* 4.1 25.6 - - + +
100E ILE* 4.6 6.5 - - + -
76G GLY* 4.9 13.0 - - - +
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Residues in contact with THR 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D GLN* 3.6 40.2 + - + +
68E THR* 3.7 14.6 - - + -
69E VAL 3.8 3.1 - - - -
70E HIS* 2.7 38.9 + - + +
78E THR* 4.1 5.9 + - - +
79E LEU* 1.3 72.9 - - - +
81E THR* 1.3 63.2 + - - +
82E LYS* 6.3 0.2 - - + -
74G ARG 3.4 9.5 - - - +
75G ASP 3.0 13.7 - - - +
76G GLY* 3.1 14.3 + - - -
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Residues in contact with THR 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E THR* 3.4 8.4 - - - +
69E VAL* 3.0 39.1 + - + +
71E PHE* 3.8 15.0 - - + -
79E LEU 5.3 0.2 - - - -
80E THR* 1.3 73.3 - - - +
82E LYS* 1.3 68.8 + - - +
92E VAL* 3.6 28.0 - - + -
96E ASN* 2.9 22.5 + - - +
98E LEU* 4.2 12.3 - - + -
74G ARG 4.2 1.3 - - - -
75G ASP* 2.5 27.6 + - - +
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Residues in contact with LYS 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E LYS* 4.3 37.0 + - + +
67E ILE 3.2 7.2 - - - +
68E THR* 4.0 14.8 - - + +
80E THR* 6.3 0.2 - - + -
81E THR* 1.3 85.4 + - - +
83E GLY* 1.3 58.6 + - - +
96E ASN* 3.0 22.7 + - - +
74G ARG* 4.6 22.2 - - + +
75G ASP* 4.1 20.8 + - - +
173G ASP* 2.7 46.1 + - + +
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Residues in contact with GLY 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E LYS* 3.6 7.4 - - - -
67E ILE* 2.7 39.7 + - - +
69E VAL* 5.3 2.2 - - - +
82E LYS* 1.3 75.5 - - - +
84E LYS* 1.3 64.9 + - - -
87E ASP* 5.3 0.2 - - - -
92E VAL* 4.1 13.1 - - - +
96E ASN* 5.0 0.2 - - - -
156E LEU* 3.8 17.0 - - - +
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Residues in contact with LYS 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E ASP 4.1 4.7 - - - +
66E LYS* 3.6 34.2 - - + +
83E GLY* 1.3 73.5 - - - -
85E VAL* 1.3 69.3 + - - +
86E GLY 3.4 0.2 + - - -
87E ASP* 3.1 42.7 + - - +
156E LEU* 3.5 8.6 - - - +
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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