Contacts of the helix formed by residues 88 - 96 (chain G) 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 SER 88 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86G GLY 3.9 1.0 + - - -
87G ASP* 1.3 74.5 - - - +
89G LEU* 1.3 64.9 + - - +
90G LEU* 3.3 10.8 + - - +
91G ASP* 3.0 48.4 + - - +
92G VAL* 3.1 12.3 + - - +
152G CYS* 3.6 23.8 + - - +
154G ILE 3.3 10.1 - - - -
155G CYS* 4.2 10.6 - - - +
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Residues in contact with LEU 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G VAL* 4.1 9.2 - - + -
71G PHE* 3.9 25.6 - - + -
88G SER* 1.3 72.2 - - - +
90G LEU* 1.3 61.5 + - - +
92G VAL* 3.2 9.6 + - + +
93G VAL* 3.1 27.2 + - - +
103G PHE* 5.0 1.1 - - - -
117G LEU* 4.0 17.7 - - + -
119G PHE* 3.7 36.8 - - + -
151G GLY 3.2 10.4 + - - +
154G ILE* 3.0 29.6 + - + +
156G LEU* 4.2 13.2 - - + -
163G MET* 3.9 23.6 - - + -
165G VAL* 4.7 2.5 - - + -
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Residues in contact with LEU 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G FES 4.0 4.9 - - - -
88G SER* 3.1 9.3 + - - +
89G LEU* 1.3 77.5 - - - +
91G ASP* 1.3 66.7 + - - +
93G VAL* 3.1 2.8 + - - +
94G VAL* 3.0 39.2 + - + +
103G PHE* 3.8 33.4 - - + +
104G GLY* 3.8 15.7 - - - +
107G GLU* 3.9 9.4 - - - -
108G GLY* 3.6 35.7 - - - +
151G GLY 3.5 4.9 + - - -
152G CYS* 3.6 18.6 - - + +
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Residues in contact with ASP 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G ASP* 4.1 16.8 - - + +
88G SER* 3.0 40.3 + - - +
90G LEU* 1.3 79.8 - - - +
92G VAL* 1.3 55.0 + - - +
94G VAL* 4.6 4.3 - - - +
95G GLU* 2.7 58.9 + - - +
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Residues in contact with VAL 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G VAL* 5.3 3.4 - - + -
71G PHE* 4.1 13.9 - - + -
81G THR* 3.6 30.3 - - + -
83G GLY* 4.1 12.3 - - - -
87G ASP* 4.5 8.1 - - + +
88G SER 3.1 13.4 + - - +
89G LEU* 3.4 15.3 - - + +
90G LEU 3.1 0.2 - - - -
91G ASP* 1.3 76.8 - - - +
93G VAL* 1.3 64.5 + - - +
95G GLU* 5.1 1.6 - - - -
96G ASN* 3.2 32.6 + - - +
98G LEU* 4.5 0.2 - - - +
156G LEU* 3.8 29.2 - - + -
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Residues in contact with VAL 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G PHE* 3.7 27.6 - - + -
89G LEU 3.1 14.1 + - - +
90G LEU* 3.1 7.0 + - + +
92G VAL* 1.3 78.2 - - - +
94G VAL* 1.3 61.0 + - + +
97G ASN* 3.1 20.6 + - - -
98G LEU* 3.2 27.4 + - + +
100G ILE* 3.8 28.9 - - + +
103G PHE* 3.7 34.8 - - + +
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Residues in contact with VAL 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G LEU* 3.0 38.1 + - + +
91G ASP* 4.0 4.5 - - - +
93G VAL* 1.3 75.8 - - + +
95G GLU* 1.3 64.7 + - + +
96G ASN 3.1 1.8 - - - -
97G ASN* 2.6 33.4 + - - +
103G PHE 5.5 3.1 - - - +
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Residues in contact with GLU 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G LYS* 4.9 11.8 + - - +
87G ASP* 4.2 17.0 - - - +
91G ASP* 2.7 43.0 + - - +
92G VAL* 4.7 1.6 - - - +
94G VAL* 1.3 79.7 - - + +
96G ASN* 1.3 67.7 + - - +
97G ASN* 3.5 3.8 + - - +
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Residues in contact with ASN 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G THR* 2.9 28.4 + - - +
82G LYS 3.0 19.6 + - - +
83G GLY* 5.0 0.2 - - - -
92G VAL* 3.2 23.4 + - - +
93G VAL 3.8 0.2 - - - -
94G VAL 3.1 0.8 - - - -
95G GLU* 1.3 86.5 + - - +
97G ASN* 1.3 72.5 + - - +
98G LEU* 3.2 14.2 + - + +
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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