Contacts of the strand formed by residues 100 - 105 (chain C) in PDB entry 3E3M
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 GLN 100 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69C GLY 3.1 14.1 + - - +
70C PHE* 3.2 9.1 - - + +
71C VAL* 2.9 28.2 + - - +
91C THR* 6.6 0.2 - - - -
94C LEU* 4.7 3.3 - - - +
95C GLU* 5.6 7.2 - - + +
98C GLY 5.7 1.1 - - - +
99C LEU* 1.3 77.3 - - - +
101C LEU* 1.3 65.4 + - - +
115D GLN* 3.1 43.0 + - - +
116D LEU* 4.0 15.2 - - + +
119D THR* 2.5 36.0 + - - +
123D ARG* 5.2 3.1 + - - -
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Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C PHE* 5.1 0.4 - - - -
71C VAL* 3.5 18.6 - - + +
73C LEU* 4.1 13.2 - - + -
87C ALA* 3.9 12.3 - - + +
90C LEU* 3.8 26.5 - - + -
91C THR* 3.4 31.2 - - + +
94C LEU* 3.7 24.7 - - + -
100C GLN* 1.3 75.0 - - - +
102C LEU* 1.3 60.1 + - - +
103C LEU* 3.9 27.3 + - + +
103D LEU 4.5 3.1 - - - +
104D GLY* 4.9 2.3 - - - -
105D TYR* 5.3 3.9 + - + -
116D LEU* 4.0 21.1 - - - +
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Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C PHE* 3.7 41.2 - - + -
71C VAL 3.0 6.9 + - - -
72C GLY* 3.4 3.8 - - - -
73C LEU 2.9 24.3 + - - +
100C GLN 4.1 0.2 + - - -
101C LEU* 1.3 75.5 - - - +
103C LEU* 1.3 65.7 + - - +
120C MET* 4.0 17.5 - - + +
123C ARG* 5.8 3.8 - - - -
70D PHE* 5.9 0.7 - - + -
102D LEU* 4.1 34.3 - - + -
103D LEU 3.7 15.5 - - - +
116D LEU* 6.6 0.2 - - + -
120D MET* 4.6 18.4 - - + -
123D ARG* 5.0 17.0 - - - +
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Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C LEU* 3.3 43.1 - - + +
75C LEU* 4.9 7.0 - - + -
78C LEU* 5.4 0.7 - - + -
101C LEU* 3.9 19.7 - - + +
102C LEU* 1.3 74.3 - - - +
104C GLY* 1.3 59.8 + - - +
120C MET* 4.9 0.9 - - - -
78D LEU* 3.7 39.7 - - + -
102D LEU* 3.7 10.7 - - - +
103D LEU* 2.8 62.2 + - + +
104D GLY* 5.1 0.2 - - - -
105D TYR* 3.8 18.8 - - + +
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Residues in contact with GLY 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C LEU 2.9 9.1 + - - +
74C LEU* 3.5 22.2 - - - +
75C LEU* 3.1 26.9 + - - +
102C LEU 4.2 0.2 + - - -
103C LEU* 1.3 77.3 - - - +
105C TYR* 1.3 60.6 + - - -
116C LEU* 3.9 15.5 - - - -
120C MET* 4.3 3.7 - - - +
101D LEU 5.0 1.6 - - - -
102D LEU* 4.7 1.1 - - - -
103D LEU* 5.2 0.7 - - - -
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Residues in contact with TYR 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C LEU* 3.5 8.7 - - - -
76C PRO 3.3 25.9 + - - -
77C SER* 3.7 9.2 - - - -
78C LEU* 3.7 30.3 + - + -
104C GLY* 1.3 71.7 - - - -
106C THR* 1.3 60.3 + - - +
107C ALA* 3.5 17.3 - - + +
112C ARG* 3.4 18.4 - - - -
116C LEU* 3.5 8.2 - - - +
84D ALA* 4.2 12.4 + - - +
87D ALA* 4.1 12.1 - - + -
88D GLN* 2.6 46.2 + - - -
91D THR* 4.6 10.2 + - - +
101D LEU* 5.2 3.9 + - + -
103D LEU* 4.1 24.8 - - + +
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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