Contacts of the helix formed by residues 101 - 108 (chain A) in PDB entry 1CEZ
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 THR 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A LYS* 6.0 0.7 - - - +
99A ARG 3.4 2.6 + - - -
100A PRO* 1.3 71.4 - - - +
102A ALA* 1.3 64.6 + - - +
104A GLN* 3.1 25.3 + - + +
105A PHE* 3.3 14.1 - - + -
208A ASP* 3.3 26.5 - - - +
211A HIS* 3.5 32.4 + - + +
105N A 4.3 0.2 + - - -
106N C 3.0 20.8 + - - -
107N G 4.6 1.7 + - - -
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Residues in contact with ALA 102 (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 TRP* 4.0 5.8 - - + -
100A PRO* 3.1 1.9 + - + +
101A THR* 1.3 78.4 - - - +
103A PHE* 1.3 62.0 + - - +
105A PHE* 3.2 6.1 + - - +
106A LEU* 3.0 26.9 + - + +
211A HIS* 3.7 15.2 + - + +
212A VAL* 4.1 15.4 - - - +
215A ARG* 3.3 47.6 - - + -
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Residues in contact with PHE 103 (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 TRP* 3.5 17.6 - + + -
89A PHE* 3.7 40.6 - + + -
92A VAL* 3.7 35.0 - - + -
93A LYS* 3.8 22.2 - - + -
99A ARG* 4.0 21.3 - - + -
100A PRO* 2.9 21.9 + - + +
102A ALA* 1.3 79.0 - - - +
104A GLN* 1.3 68.7 + - - +
106A LEU* 4.5 1.1 - - - +
107A GLN* 2.8 67.3 + - + +
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Residues in contact with GLN 104 (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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98A LYS* 6.3 0.2 - - - +
99A ARG* 4.3 19.4 + - - +
100A PRO 3.8 7.9 - - - +
101A THR* 3.3 21.3 - - + +
103A PHE* 1.3 88.6 - - - +
105A PHE* 1.3 70.8 + - + +
107A GLN* 3.9 19.0 + - - +
108A GLU* 4.7 6.8 - - - +
16T T 5.4 5.3 + - - -
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Residues in contact with PHE 105 (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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101A THR* 3.3 25.1 - - + -
102A ALA 3.2 2.4 + - - +
104A GLN* 1.3 83.4 - - + +
106A LEU* 1.3 62.2 + - - +
107A GLN 3.4 0.5 + - - -
108A GLU* 3.6 12.1 + - - +
109A ILE* 3.0 16.8 - - - +
149A ALA* 5.6 0.9 - - - +
204A TRP* 3.5 56.3 - + + -
208A ASP* 3.2 45.8 - - + -
212A VAL* 3.9 14.1 - - + -
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Residues in contact with LEU 106 (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 TRP* 3.9 27.8 - - + -
89A PHE* 3.7 11.9 - - + -
102A ALA* 3.0 27.1 + - + +
103A PHE 4.2 0.9 - - - +
105A PHE* 1.3 73.1 - - - +
107A GLN* 1.3 66.1 + - - +
108A GLU 3.0 4.5 + - - -
109A ILE* 3.0 26.4 + - + +
114A VAL* 4.1 25.5 - - + +
145A ILE* 3.8 17.9 - - + -
212A VAL* 3.6 30.5 - - + +
215A ARG* 4.5 2.9 - - + -
216A CYS* 4.0 18.2 - - - -
219A MET* 4.5 4.5 - - + -
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Residues in contact with GLN 107 (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 PHE* 4.0 21.6 - - + -
93A LYS* 4.8 10.5 - - - +
103A PHE* 2.8 60.1 + - + +
104A GLN* 3.9 20.9 + - - +
106A LEU* 1.3 72.5 - - - +
108A GLU* 1.3 74.6 + - - +
109A ILE 4.5 1.6 - - - +
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Residues in contact with GLU 108 (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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104A GLN 4.7 7.9 - - - +
105A PHE 3.6 10.1 + - - +
106A LEU 3.1 1.2 - - - -
107A GLN* 1.3 95.1 - - + +
109A ILE* 1.3 64.2 + - + +
110A LYS 3.8 1.0 + - - -
149A ALA* 6.2 1.8 - - + -
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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