Contacts of the helix formed by residues 102 - 111 (chain E) in PDB entry 7CR3
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 SER 102 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E ILE* 1.3 75.9 - - - +
103E ALA* 1.3 64.3 + - - +
104E ALA* 3.7 7.0 + - - +
105E GLU* 3.0 23.8 + - - +
106E LEU* 3.0 21.5 + - - +
135E GLY 3.7 4.7 - - - -
136E GLN* 5.0 2.2 - - - +
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Residues in contact with ALA 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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102E SER* 1.3 72.2 - - - +
104E ALA* 1.3 58.0 + - - +
106E LEU* 3.2 14.2 + - - +
107E ARG* 3.0 57.4 + - - +
126E ILE* 4.0 14.7 - - + +
135E GLY* 2.9 32.5 + - - +
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Residues in contact with ALA 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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102E SER* 3.2 6.3 + - - +
103E ALA* 1.3 76.2 - - - +
105E GLU* 1.3 57.8 + - - +
107E ARG* 3.2 23.2 + - - +
108E HIS* 2.9 28.9 + - - +
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Residues in contact with GLU 105 (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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95E LYS* 3.9 17.5 + - + +
101E ILE* 3.7 19.3 - - + -
102E SER* 3.0 23.7 + - - +
104E ALA* 1.3 74.9 - - - +
106E LEU* 1.3 65.6 + - - +
108E HIS* 4.0 16.0 - - - +
109E VAL* 2.9 47.3 + - + +
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Residues in contact with LEU 106 (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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90E PHE* 5.8 7.6 - - + -
101E ILE* 3.6 33.4 - - + +
102E SER 3.0 10.4 + - - +
103E ALA* 3.2 18.6 + - - +
105E GLU* 1.3 75.1 - - - +
107E ARG* 1.3 57.0 + - - +
109E VAL* 5.1 2.0 - - - -
110E MET* 2.8 42.5 + - + +
122E VAL* 4.1 5.8 - - + -
126E ILE* 3.8 21.3 - - + -
129E ALA* 6.2 0.9 - - + -
137E VAL* 3.6 31.2 - - + -
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Residues in contact with ARG 107 (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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103E ALA* 3.0 31.7 + - - +
104E ALA* 3.2 34.5 - - - +
105E GLU 3.3 0.2 - - - -
106E LEU* 1.3 74.7 - - - +
108E HIS* 1.3 57.8 + - - +
111E THR* 2.2 39.6 + - + +
119E ASP* 6.4 0.4 - - + -
122E VAL* 3.7 33.4 - - + +
123E ASP* 3.0 23.5 + - - +
126E ILE* 3.3 15.0 - - + +
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Residues in contact with HIS 108 (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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104E ALA 2.9 20.8 + - - +
105E GLU* 3.8 18.4 - - - +
107E ARG* 1.3 75.6 - - - +
109E VAL* 1.3 81.8 + - + +
111E THR* 3.7 2.8 + - - -
112E ASN* 3.2 43.3 + - + +
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Residues in contact with VAL 109 (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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337D ALA* 4.6 3.8 - - + -
93E PHE* 3.5 34.1 - - + -
95E LYS* 4.5 8.5 - - - +
105E GLU* 2.9 43.9 + - + +
106E LEU* 4.3 1.8 - - - +
108E HIS* 1.3 85.4 - - + +
110E MET* 1.3 67.7 + - + +
112E ASN* 3.1 1.6 + - - -
113E LEU* 2.9 45.5 + - + +
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Residues in contact with MET 110 (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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337D ALA* 4.1 9.0 - - - +
340D ILE* 3.6 35.7 - - + -
341D GLN* 2.9 62.3 + - + +
90E PHE* 6.1 0.7 - - + -
106E LEU* 2.8 31.4 + - + +
109E VAL* 1.3 77.4 - - + +
111E THR* 1.3 58.7 + - + +
112E ASN 3.3 0.4 + - - -
113E LEU* 5.2 0.2 - - - -
116E LYS* 3.5 6.2 - - - -
117E LEU* 4.0 3.7 + - + -
122E VAL* 4.1 11.9 - - + -
125E MET* 3.7 34.3 - - + +
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Residues in contact with THR 111 (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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107E ARG* 2.2 33.6 + - + +
108E HIS* 3.7 4.0 + - - -
110E MET* 1.3 75.8 - - + +
112E ASN* 1.3 59.2 + - - +
116E LYS* 3.3 23.4 - - - +
117E LEU* 3.3 23.2 - - + +
118E THR 3.5 18.8 - - - +
119E ASP* 5.1 0.7 - - - -
122E VAL* 3.7 20.0 - - + -
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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