Contacts of the helix formed by residues 93 - 104 (chain E) in PDB entry 2P1N
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 VAL 93 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73E LEU* 4.6 3.8 - - + -
91E GLY 3.6 0.4 + - - -
92E TYR* 1.3 71.3 - - - +
94E TYR* 1.3 71.0 + - - +
95E PRO* 3.2 3.1 - - - -
96E TRP* 2.7 30.5 + - + +
97E ILE* 3.0 33.5 + - + +
100E MET* 6.3 0.2 - - + -
112E LEU* 3.8 40.6 - - + -
115E MET* 3.8 16.2 - - + -
116E VAL 3.2 17.0 + - - +
117E VAL* 4.2 8.7 - - + -
121E CYS* 3.9 12.3 - - - -
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Residues in contact with TYR 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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92E TYR* 3.4 4.4 - - + +
93E VAL* 1.3 81.8 - - - +
95E PRO* 1.4 75.9 - - + +
96E TRP 2.8 0.7 + - - -
97E ILE* 3.0 5.0 + - + +
98E GLU* 2.8 47.4 + - + -
116E VAL 4.7 0.2 + - - -
118E THR* 5.1 2.9 - - + +
120E ASP* 4.3 15.7 - - + -
121E CYS* 3.8 39.8 - - - -
124E LEU* 4.1 26.8 - - + +
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Residues in contact with PRO 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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58E PRO* 4.4 15.7 - - + +
92E TYR* 3.4 26.5 - - + +
94E TYR* 1.4 94.7 - - + +
96E TRP* 1.3 66.1 + - + +
98E GLU* 3.0 10.8 + - + +
99E ALA* 3.0 24.9 + - - +
568E ASP* 6.0 1.3 - - - +
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Residues in contact with TRP 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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50E ILE* 4.1 18.2 - - + -
53E CYS* 3.5 27.7 + - + +
54E TYR* 6.2 0.8 - - - -
56E VAL* 3.4 30.5 - - + -
58E PRO* 3.5 45.2 - - + +
61E VAL* 3.9 26.5 - - + -
62E ILE* 5.9 0.7 - - + -
71E VAL* 5.4 1.3 - - + -
73E LEU* 4.0 29.4 - - + -
92E TYR 4.0 18.8 + - - -
93E VAL* 2.7 23.7 + - + +
95E PRO* 1.3 84.0 - - + +
97E ILE* 1.3 61.4 + - + +
99E ALA* 3.3 2.1 + - - +
100E MET* 3.0 43.3 + - + +
115E MET* 5.2 0.9 - - + -
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Residues in contact with ILE 97 (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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93E VAL* 3.0 44.8 + - + +
94E TYR* 3.0 9.5 + - - +
96E TRP* 1.3 77.5 - - + +
98E GLU* 1.3 67.6 + - - +
100E MET* 4.1 13.8 - - + +
101E SER* 3.0 21.7 + - - -
110E ILE* 5.3 2.0 - - + -
112E LEU* 5.2 3.8 - - + -
121E CYS* 4.3 14.1 - - + +
124E LEU* 3.4 34.8 - - + +
125E ILE* 3.7 34.1 - - + +
129E PHE* 5.0 4.5 - - + -
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Residues in contact with GLU 98 (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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94E TYR* 2.8 37.9 + - + +
95E PRO* 3.4 13.0 - - + +
97E ILE* 1.3 74.8 - - - +
99E ALA* 1.3 62.9 - - - +
101E SER* 2.8 21.5 + - - -
102E SER* 4.0 3.8 + - - -
124E LEU* 4.0 13.3 - - - +
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Residues in contact with ALA 99 (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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58E PRO* 4.0 12.3 - - + -
59E ALA* 5.4 1.3 - - - +
62E ILE* 3.2 28.3 - - + +
95E PRO 3.0 16.1 + - - +
96E TRP 3.7 2.9 - - - +
98E GLU* 1.3 78.6 - - + +
100E MET* 1.3 65.3 + - - +
101E SER 3.3 0.5 + - - -
102E SER* 3.7 9.6 + - - -
103E SER* 3.6 17.5 + - - -
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Residues in contact with MET 100 (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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62E ILE* 4.6 8.7 - - + -
71E VAL* 3.7 35.0 - - + -
73E LEU* 5.6 1.6 - - + -
93E VAL* 6.3 0.2 - - + -
96E TRP* 3.0 36.1 + - + +
97E ILE* 3.2 14.1 + - + +
99E ALA* 1.3 79.1 - - - +
101E SER* 1.3 62.8 + - - +
103E SER 3.0 1.2 + - - +
104E TYR* 2.9 56.8 + - + +
107E LEU* 3.7 20.9 - - + -
110E ILE* 4.2 17.7 - - + -
129E PHE* 4.2 11.4 - - + -
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Residues in contact with SER 101 (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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97E ILE* 3.0 13.5 + - - -
98E GLU* 2.8 21.0 + - - -
100E MET* 1.3 76.5 - - - +
102E SER* 1.3 60.4 + - - +
105E THR* 4.4 17.3 - - - +
124E LEU* 4.3 13.5 - - - +
128E SER* 3.1 41.3 - - - +
129E PHE* 4.2 5.8 - - - -
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Residues in contact with SER 102 (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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98E GLU 4.0 2.6 + - - -
99E ALA* 3.7 11.9 + - - -
101E SER* 1.3 83.0 + - - +
103E SER* 1.3 65.7 + - - +
105E THR* 4.5 9.5 + - - +
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Residues in contact with SER 103 (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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62E ILE* 3.2 34.4 - - - +
66E PRO* 4.5 6.4 - - - +
99E ALA 3.6 8.2 + - - -
100E MET 3.0 6.1 + - - -
102E SER* 1.3 80.7 + - - +
104E TYR* 1.3 68.8 + - - +
105E THR* 3.3 6.9 + - - -
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Residues in contact with TYR 104 (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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61E VAL* 3.6 13.8 + - + +
62E ILE* 3.5 34.8 - - + -
65E PHE 2.6 30.1 + - - -
66E PRO* 3.4 20.9 - - + -
68E VAL* 3.5 37.4 - - + +
71E VAL* 4.3 6.1 - - + -
100E MET* 2.9 47.8 + - + +
103E SER* 1.3 83.0 - - - +
105E THR* 1.3 55.4 + - - +
106E TRP* 2.9 13.9 + - - -
107E LEU* 3.0 25.4 + - + +
129E PHE* 3.3 12.1 - - - -
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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