Contacts of the helix formed by residues 112 - 123 (chain A) in PDB entry 5H5Q
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 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A GLY* 1.3 76.4 - - - -
113A ASN* 1.3 65.7 + - - +
114A GLU* 3.5 8.9 + - - +
115A GLU* 2.9 39.9 + - - +
116A ILE* 2.9 22.2 + - - +
132A LYS* 5.4 0.2 - - - +
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Residues in contact with ASN 113 (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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49A ILE* 3.5 27.4 - - + +
112A SER* 1.3 73.2 - - - +
114A GLU* 1.3 57.8 + - - +
116A ILE* 3.3 6.7 + - - +
117A LYS* 2.8 31.1 + - - +
130A PHE 4.6 0.2 - - - +
131A SER* 3.5 26.1 + - - -
132A LYS* 2.9 37.2 + - - +
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Residues in contact with GLU 114 (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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49A ILE 5.0 0.8 + - - -
50A ASP* 5.1 1.4 - - - +
112A SER* 3.2 8.7 + - - +
113A ASN* 1.3 79.0 - - - +
115A GLU* 1.3 58.5 + - + +
117A LYS* 3.3 22.8 + - - +
118A GLU* 2.7 62.3 + - - +
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Residues in contact with GLU 115 (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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111A GLY* 3.3 12.7 - - - -
112A SER* 2.9 38.5 + - - +
114A GLU* 1.3 77.7 - - + +
116A ILE* 1.3 58.1 + - - +
118A GLU* 3.3 10.4 + - - +
119A PHE* 2.9 27.8 + - - +
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Residues in contact with ILE 116 (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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49A ILE* 3.8 7.2 - - + -
71A SER* 4.7 4.3 - - - +
80A TYR* 4.7 3.4 - - - +
101A PRO* 3.8 24.0 - - + -
109A GLU* 3.6 48.9 - - + +
111A GLY* 3.6 19.7 - - - +
112A SER 2.9 23.7 + - - +
113A ASN* 3.7 10.5 - - - +
115A GLU* 1.3 73.2 - - - +
117A LYS* 1.3 66.2 + - - +
119A PHE* 3.2 7.2 + - + +
120A ALA* 2.9 23.6 + - - +
129A MET* 4.2 8.7 - - + -
132A LYS* 3.8 10.3 - - - -
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Residues in contact with LYS 117 (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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49A ILE* 3.6 28.2 - - + +
50A ASP* 2.7 37.2 + - - +
113A ASN 2.8 17.5 + - - +
114A GLU* 3.4 23.5 + - - +
116A ILE* 1.3 76.7 - - - +
118A GLU* 1.3 58.6 + - + +
120A ALA* 3.4 4.8 + - - +
121A ALA* 2.9 30.3 + - + +
129A MET* 5.4 3.1 - - + -
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Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A GLU* 2.7 46.9 + - - +
115A GLU* 3.7 8.5 - - - +
116A ILE 3.3 0.2 - - - -
117A LYS* 1.3 77.4 - - + +
119A PHE* 1.3 62.9 + - - +
121A ALA* 3.3 8.3 + - - +
122A GLY* 3.1 17.8 + - - -
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Residues in contact with PHE 119 (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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71A SER* 3.4 47.6 - - - +
76A THR* 3.6 25.4 - - + -
80A TYR* 4.0 15.3 - + - -
115A GLU 2.9 14.9 + - - +
116A ILE* 3.2 9.6 + - + +
118A GLU* 1.3 76.4 - - - +
120A ALA* 1.3 65.7 + - - +
122A GLY* 3.1 14.9 + - - -
123A TYR* 3.7 32.9 + + - -
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Residues in contact with ALA 120 (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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80A TYR* 3.9 21.3 - - + +
116A ILE 2.9 15.4 + - - +
117A LYS 3.8 3.8 - - - +
119A PHE* 1.3 78.3 - - - +
121A ALA* 1.3 63.8 + - - +
123A TYR* 3.0 12.7 + - - +
125A VAL* 3.2 25.5 + - + +
129A MET* 3.7 36.8 - - + -
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Residues in contact with ALA 121 (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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117A LYS* 2.9 19.2 + - + +
118A GLU* 3.6 9.4 - - - +
119A PHE 3.3 0.2 - - - -
120A ALA* 1.3 76.6 - - - +
122A GLY* 1.3 58.0 + - - +
124A ASN* 2.9 21.3 + - - +
125A VAL* 4.5 8.7 - - - +
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Residues in contact with GLY 122 (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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118A GLU 3.1 9.0 + - - -
119A PHE 3.1 11.4 + - - -
121A ALA* 1.3 77.0 - - - +
123A TYR* 1.3 60.4 + - - +
124A ASN 3.3 1.2 + - - -
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Residues in contact with TYR 123 (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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76A THR* 4.8 1.5 - - + +
77A GLU* 3.5 33.8 + - + +
80A TYR* 3.9 27.4 - + + -
81A THR* 3.8 30.9 - - + -
84A VAL* 3.5 17.8 - - + +
119A PHE* 3.7 44.6 - + - -
120A ALA 3.0 9.3 + - - +
122A GLY* 1.3 79.0 - - - +
124A ASN* 1.3 69.6 + - - +
125A VAL* 3.2 9.8 + - + -
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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