Contacts of the helix formed by residues 88 - 96 (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 SER 88 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E GLY 3.9 1.4 + - - -
87E ASP* 1.3 74.7 - - - +
89E LEU* 1.3 64.8 + - - +
90E LEU* 3.3 9.9 + - - +
91E ASP* 2.9 49.2 + - - +
92E VAL* 3.1 12.4 + - - +
152E CYS* 3.6 23.7 + - - +
154E ILE 3.3 9.6 - - - -
155E CYS* 4.2 10.5 - - - +
156E LEU* 5.3 0.2 - - - -
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Residues in contact with LEU 89 (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* 4.1 9.6 - - + -
71E PHE* 3.9 26.0 - - + -
88E SER* 1.3 71.7 - - - +
90E LEU* 1.3 60.0 + - - +
92E VAL* 3.3 9.6 + - + +
93E VAL* 3.1 28.0 + - - +
103E PHE* 5.0 0.9 - - - -
117E LEU* 3.9 16.6 - - + -
119E PHE* 3.7 36.8 - - + -
151E GLY 3.1 11.6 + - - +
154E ILE* 3.0 30.8 + - + +
156E LEU* 4.2 14.1 - - + -
163E MET* 3.9 23.1 - - + -
165E VAL* 4.7 2.2 - - + -
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Residues in contact with LEU 90 (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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6E FES 4.0 5.4 - - - -
88E SER* 3.1 8.4 + - - +
89E LEU* 1.3 75.5 - - - +
91E ASP* 1.3 69.5 + - - +
93E VAL* 3.0 3.6 + - + +
94E VAL* 2.9 39.9 + - + +
103E PHE* 3.8 32.3 - - + +
104E GLY* 3.9 14.8 - - - +
107E GLU* 3.8 10.5 - - - +
108E GLY* 3.6 35.0 - - - +
151E GLY 3.5 5.3 + - - -
152E CYS* 3.6 19.3 - - + +
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Residues in contact with ASP 91 (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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87E ASP* 4.0 21.5 - - + +
88E SER* 2.9 42.7 + - - +
90E LEU* 1.3 78.8 - - - +
92E VAL* 1.3 54.1 + - - +
94E VAL* 4.7 4.3 - - - -
95E GLU* 2.7 46.3 + - + +
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Residues in contact with VAL 92 (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* 5.3 4.3 - - + -
71E PHE* 4.1 14.1 - - + -
81E THR* 3.6 30.1 - - + -
82E LYS 4.7 2.7 - - - +
83E GLY* 4.1 10.8 - - - -
87E ASP* 4.5 7.6 - - + +
88E SER 3.1 12.2 + - - +
89E LEU* 3.5 12.8 - - + +
90E LEU 3.1 0.2 - - - -
91E ASP* 1.3 76.4 - - - +
93E VAL* 1.3 63.3 + - - +
95E GLU* 5.0 1.8 - - - -
96E ASN* 3.2 33.2 + - - +
98E LEU* 4.5 0.2 - - - +
156E LEU* 3.7 30.1 - - + -
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Residues in contact with VAL 93 (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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71E PHE* 3.7 26.9 - - + -
89E LEU 3.1 15.5 + - - +
90E LEU* 3.0 7.5 + - + +
92E VAL* 1.3 76.1 - - - +
94E VAL* 1.3 65.2 + - + +
97E ASN* 3.1 17.8 + - - -
98E LEU* 3.3 25.8 + - + +
100E ILE* 3.9 28.5 - - + +
103E PHE* 3.7 35.0 - - + +
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Residues in contact with VAL 94 (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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90E LEU* 2.9 37.1 + - + +
91E ASP* 4.0 4.3 - - - +
93E VAL* 1.3 77.9 - - + +
95E GLU* 1.3 72.2 + - + +
96E ASN 3.1 2.0 - - - -
97E ASN* 3.1 25.8 + - - +
103E PHE 5.5 3.1 - - - +
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Residues in contact with GLU 95 (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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87E ASP* 5.5 5.6 - - - +
91E ASP* 2.7 32.4 + - + +
92E VAL* 4.6 1.6 - - - +
94E VAL* 1.3 79.0 - - + +
96E ASN* 1.3 67.6 + - - +
97E ASN* 3.5 2.5 - - - +
77G GLU* 5.5 0.5 - - - +
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Residues in contact with ASN 96 (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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81E THR* 2.9 27.3 + - - +
82E LYS 3.0 19.7 + - - +
92E VAL* 3.2 23.1 + - - +
94E VAL 3.1 0.6 - - - -
95E GLU* 1.3 85.8 + - - +
97E ASN* 1.3 68.5 + - - +
98E LEU* 3.3 12.2 + - + +
75G ASP* 3.6 24.4 + - + +
77G GLU* 3.3 25.5 - - - +
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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