Contacts of the helix formed by residues 85 - 93 (chain A) in PDB entry 2P3L
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 GLY 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A VAL* 3.7 4.9 - - - -
82A CYS* 3.0 16.8 + - - -
83A GLY 3.1 1.5 - - - -
84A ARG* 1.3 80.0 - - - +
86A GLY* 1.3 60.7 + - - +
87A TRP 3.4 2.7 - - - -
88A SER* 3.1 9.1 + - - -
89A TYR* 2.9 34.8 + - - -
126A LEU* 4.0 16.6 - - - -
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Residues in contact with GLY 86 (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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55A VAL* 3.3 17.4 - - - +
56A SER* 3.7 7.2 - - - -
59A SER* 2.6 30.1 + - - -
85A GLY* 1.3 75.0 - - - +
87A TRP* 1.3 62.7 + - - +
89A TYR* 4.4 0.8 - - - +
90A TYR* 3.4 14.6 + - - +
1001A SAH 3.2 20.1 + - - -
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Residues in contact with TRP 87 (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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58A GLY* 2.9 33.1 + - - -
61A LYS* 4.5 7.6 - - + +
62A LEU* 3.7 34.3 - - + +
65A PHE* 5.2 2.5 - + - -
79A ASP* 3.5 19.7 + - - +
85A GLY 3.4 0.6 - - - -
86A GLY* 1.3 71.8 - - - +
88A SER* 1.3 59.6 + - - +
90A TYR* 3.4 3.6 + - - +
91A CYS* 2.9 35.3 + - - +
144A LEU* 3.7 26.5 - - + -
145A CYS 3.8 10.1 - - - -
146A ASP* 3.6 23.6 + - + -
179A CYS* 3.8 29.6 - - + -
219A TYR* 3.5 36.3 - + - -
1001A SAH 3.2 30.4 + - - +
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Residues in contact with SER 88 (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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79A ASP* 2.9 32.1 + - - +
82A CYS* 4.2 0.3 - - - +
85A GLY* 3.1 8.6 + - - -
87A TRP* 1.3 77.0 - - - +
89A TYR* 1.3 58.5 + - - +
91A CYS* 3.1 6.0 + - - +
92A GLY* 2.9 26.2 + - - -
100A VAL* 3.5 21.6 - - - +
102A GLY* 3.9 0.9 - - - -
124A VAL* 3.9 10.5 - - - +
126A LEU* 3.6 30.2 - - - +
144A LEU* 5.8 0.2 - - - -
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Residues in contact with TYR 89 (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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53A HIS 5.9 0.2 - - - +
55A VAL* 4.1 14.8 - - + +
84A ARG 3.9 5.4 - - - -
85A GLY 2.9 28.7 + - - +
86A GLY* 4.4 2.2 - - - +
88A SER* 1.3 72.3 - - - +
90A TYR* 1.3 64.6 + - - +
92A GLY* 3.1 13.8 + - - +
93A GLY 3.5 3.5 + - - -
114A ILE 2.5 30.7 + - - -
115A PRO* 3.4 4.5 - - - +
116A MET* 3.2 34.9 + - + -
118A THR* 3.9 23.4 + - - +
119A TYR 4.3 6.1 - - - +
121A TRP* 4.3 13.2 - - + -
124A VAL* 4.1 23.8 - - + -
126A LEU* 3.6 23.7 - - + +
258A LEU* 4.2 15.6 - - + +
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Residues in contact with TYR 90 (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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59A SER* 4.1 15.9 - - - +
62A LEU* 3.7 22.7 - - + -
63A ARG* 3.7 36.6 + - + +
66A VAL* 3.8 29.1 - - + +
67A GLU* 5.0 1.7 + - - +
86A GLY 3.4 17.6 + - - +
87A TRP* 3.4 5.6 - - - +
88A SER 3.2 0.2 - - - -
89A TYR* 1.3 80.6 - - - +
91A CYS* 1.3 61.6 + - - +
93A GLY* 3.2 10.6 + - - -
94A LEU* 3.6 40.1 - - + +
256A VAL* 4.2 13.9 - - + -
258A LEU* 3.7 27.1 - - + +
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Residues in contact with CYS 91 (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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62A LEU* 3.7 11.9 - - - -
73A PRO* 3.8 25.1 - - + -
77A VAL* 4.3 9.4 - - + -
87A TRP 2.9 22.6 + - - +
88A SER* 3.5 6.1 - - - +
90A TYR* 1.3 73.2 - - - +
92A GLY* 1.3 62.5 + - - +
94A LEU* 3.1 20.3 + - + -
97A VAL* 3.3 19.1 - - - +
100A VAL* 3.9 15.0 - - + -
144A LEU* 3.6 28.0 - - - -
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Residues in contact with GLY 92 (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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88A SER 2.9 13.3 + - - -
89A TYR 3.1 7.4 + - - -
91A CYS* 1.3 75.3 - - - +
93A GLY* 1.3 55.8 + - - +
94A LEU 3.4 0.2 - - - -
97A VAL* 4.6 2.7 - - - -
100A VAL* 4.0 5.4 - - - +
119A TYR 3.6 7.2 - - - -
120A GLY* 3.4 9.2 - - - +
123A LEU* 4.0 3.9 - - - +
124A VAL* 3.8 19.7 - - - -
263A ARG* 3.0 28.7 + - - -
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Residues in contact with GLY 93 (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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89A TYR 3.5 2.4 + - - -
90A TYR 3.2 8.4 + - - -
91A CYS 3.1 1.2 - - - -
92A GLY* 1.3 77.1 - - - +
94A LEU* 1.3 67.0 + - - +
95A LYS 3.8 1.4 + - - -
119A TYR* 3.4 41.9 + - - -
258A LEU 6.0 0.2 - - - -
263A ARG* 3.7 3.5 - - - -
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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