Contacts of the helix formed by residues 100 - 107 (chain H) in PDB entry 2A27
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 GLU 100 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53F ARG* 5.4 5.2 + - - -
98H GLY 4.4 0.9 - - - +
99H GLY* 1.3 75.7 - - - +
101H LEU* 1.3 65.9 + - - +
102H PHE* 4.1 7.0 - - - +
103H ASP* 3.5 12.5 + - + +
104H PHE* 3.5 13.0 + - - +
142H PRO* 3.6 20.6 - - - +
143H GLU* 3.7 39.2 - - - +
145H ILE 3.6 5.4 - - - -
146H MET* 3.9 8.0 - - - -
147H LEU* 3.8 6.7 - - - +
150H LYS* 5.2 0.2 + - - -
300H TYR* 3.5 28.5 + - - +
305H SER 5.3 5.5 - - - +
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Residues in contact with LEU 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H GLY 3.9 0.2 + - - -
100H GLU* 1.3 72.2 - - - +
102H PHE* 1.3 82.3 + - + +
104H PHE* 2.9 18.2 + - + +
105H LEU* 3.0 35.9 + - + +
119H PHE* 4.1 23.8 - - + -
123H ILE* 4.1 10.5 - - + -
142H PRO 4.6 0.6 + - - +
145H ILE* 3.0 42.3 + - + +
147H LEU* 3.7 26.3 - - + +
157H ILE* 3.9 10.3 - - + -
210H LEU* 4.4 11.2 - - + -
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Residues in contact with PHE 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H GLU* 3.4 4.1 - - - +
101H LEU* 1.3 92.8 - - + +
103H ASP* 1.3 55.8 + - - +
105H LEU* 3.8 4.5 - - + -
106H ALA* 3.1 24.6 + - - +
142H PRO* 3.5 45.5 + - + -
145H ILE* 5.5 0.9 - - + -
206H ILE* 3.8 31.4 - - + -
209H ILE* 3.7 23.6 - - + -
210H LEU* 4.0 27.1 - - + -
296H PHE* 3.4 32.4 - + + -
300H TYR* 3.6 23.7 - + + -
303H ARG* 4.3 9.4 - - - -
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Residues in contact with ASP 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H GLY* 5.3 1.6 - - - -
100H GLU* 3.5 19.4 + - + +
101H LEU 3.0 0.2 + - - -
102H PHE* 1.3 76.5 - - - +
104H PHE* 1.3 64.7 + - - +
106H ALA* 3.3 11.3 + - - +
107H GLN* 3.2 19.8 + - - +
150H LYS* 3.1 19.9 + - - +
300H TYR* 3.2 36.0 + - - +
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Residues in contact with PHE 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H GLU 3.5 1.8 + - - +
101H LEU* 2.9 5.7 + - + +
103H ASP* 1.3 79.9 + - - +
105H LEU* 1.3 73.0 + - + +
107H GLN* 3.2 23.5 + - + +
108H LYS* 3.6 43.7 + - + +
119H PHE* 3.9 11.2 - + - -
147H LEU* 3.4 26.2 - - + -
150H LYS* 3.6 46.8 - - + +
152H ILE 4.1 3.4 - - - -
153H PRO 3.8 4.5 - - - -
155H PRO* 3.5 31.0 - - + -
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Residues in contact with LEU 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H LEU* 3.0 34.6 + - + +
102H PHE* 3.8 14.6 - - + +
103H ASP 3.2 0.4 - - - -
104H PHE* 1.3 84.3 - - + +
106H ALA* 1.3 62.4 + - - +
107H GLN 3.2 0.2 - - - -
108H LYS* 3.3 26.9 + - + +
111H LEU* 4.7 11.2 - - + -
119H PHE* 3.9 30.7 - - + -
210H LEU* 3.7 41.5 - - + -
293H LEU* 3.6 17.3 - - + +
296H PHE* 4.0 12.1 - - + -
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Residues in contact with ALA 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102H PHE 3.1 16.9 + - - +
103H ASP 3.6 6.1 - - - +
104H PHE 3.2 0.4 - - - -
105H LEU* 1.3 75.5 - - - +
107H GLN* 1.3 62.7 + - - +
108H LYS 3.2 1.1 + - - -
296H PHE* 3.9 14.8 - - + -
297H ARG* 3.4 41.9 + - + +
300H TYR* 4.2 19.5 - - + -
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Residues in contact with GLN 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H ASP* 3.2 30.3 + - - +
104H PHE* 3.2 20.4 + - + +
106H ALA* 1.3 80.2 - - - +
108H LYS* 1.3 61.3 + - - +
109H GLU* 3.3 3.5 + - - +
150H LYS* 3.9 14.7 + - - +
297H ARG* 5.1 0.7 - - - -
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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