Contacts of the helix formed by residues 127 - 140 (chain D) in PDB entry 4H7Y
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 PRO 127 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94D ALA* 3.6 9.9 - - + +
95D PHE* 5.6 0.9 - - + +
125D ALA 4.0 0.2 - - - -
126D VAL* 1.3 88.7 - - + +
128D LEU* 1.3 67.1 + - - +
129D GLU* 3.2 9.9 + - + +
130D MET* 3.3 48.1 + - + +
131D LEU 3.7 0.7 + - - -
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Residues in contact with LEU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D VAL* 4.1 35.0 - - + +
125D ALA 4.0 8.7 + - - +
126D VAL* 3.9 7.3 - - + +
127D PRO* 1.3 71.6 - - - +
129D GLU* 1.3 65.3 + - - +
131D LEU* 2.9 18.0 + - + +
132D GLU* 3.0 40.4 + - + +
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Residues in contact with GLU 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D PRO* 3.2 7.7 - - + +
128D LEU* 1.3 77.6 - - - +
130D MET* 1.3 56.6 + - - +
132D GLU* 3.2 28.1 + - - +
133D ILE* 2.9 47.1 + - + +
136D ARG* 4.0 16.4 + - - -
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Residues in contact with MET 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ALA* 4.4 3.1 - - + -
95D PHE* 3.9 30.7 - - + -
98D ILE* 3.4 29.5 - - + +
127D PRO* 3.3 37.1 + - + +
128D LEU 3.2 0.2 - - - -
129D GLU* 1.3 78.8 - - - +
131D LEU* 1.3 62.8 + - - +
133D ILE* 3.4 10.3 + - - +
134D ALA* 3.0 18.0 + - - +
146D LEU* 3.8 23.6 - - + +
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Residues in contact with LEU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ALA* 3.8 17.9 - - + +
97D HIS* 4.7 0.4 - - + -
98D ILE* 3.8 24.9 - - + -
117D LEU* 4.3 11.3 - - + +
120D ALA* 3.9 22.7 - - + -
121D VAL* 3.8 42.0 - - + +
125D ALA* 3.6 27.6 - - + +
127D PRO 4.2 0.4 - - - +
128D LEU* 2.9 14.1 + - + +
130D MET* 1.3 78.1 - - - +
132D GLU* 1.3 56.8 + - - +
134D ALA* 3.2 4.4 + - - +
135D LEU* 2.9 35.4 + - + +
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Residues in contact with GLU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D VAL* 5.7 1.1 - - + -
128D LEU* 3.0 44.8 + - + +
129D GLU* 3.2 31.5 - - - +
131D LEU* 1.3 76.2 - - - +
133D ILE* 1.3 60.4 + - - +
135D LEU* 3.7 11.3 + - + +
136D ARG* 3.2 43.9 + - - +
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Residues in contact with ILE 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D GLU* 2.9 36.6 + - + +
130D MET* 3.7 8.3 - - - +
132D GLU* 1.3 75.4 - - - +
134D ALA* 1.3 62.8 + - - +
136D ARG* 3.3 25.4 + - - +
137D ASN* 2.4 48.1 + - - +
145D LEU 4.2 0.2 - - - +
146D LEU* 3.8 19.5 - - + -
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Residues in contact with ALA 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ILE* 4.1 11.2 - - + -
117D LEU* 3.9 23.1 - - + -
130D MET 3.0 14.9 + - - +
131D LEU 3.6 6.5 - - - +
133D ILE* 1.3 76.2 - - - +
135D LEU* 1.3 58.2 + - - +
137D ASN* 3.3 1.0 + - - -
138D LEU* 2.8 29.8 + - - +
145D LEU* 3.5 35.9 - - + +
146D LEU* 4.4 1.1 - - + +
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D LYS* 4.4 17.5 - - + -
117D LEU* 3.7 33.0 - - + +
118D GLN* 4.2 20.4 - - + +
121D VAL* 4.1 23.8 - - + -
131D LEU 2.9 19.7 + - - +
132D GLU* 3.9 9.6 - - + +
134D ALA* 1.3 77.6 - - - +
136D ARG* 1.3 56.9 + - + +
138D LEU* 3.4 6.3 - - + +
139D ASN* 3.0 41.4 + - - +
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Residues in contact with ARG 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D GLU* 4.0 12.5 + - - -
132D GLU* 3.2 31.5 + - - +
133D ILE* 3.6 32.6 - - - +
134D ALA 3.3 0.4 - - - -
135D LEU* 1.3 73.9 - - + +
137D ASN* 1.3 62.7 + - - +
139D ASN* 3.2 7.7 + - - +
140D LEU* 2.9 41.2 + - + +
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Residues in contact with ASN 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ILE* 2.4 54.7 + - - +
134D ALA 3.8 1.3 - - - +
136D ARG* 1.3 77.6 - - - +
138D LEU* 1.3 58.3 + - - +
140D LEU* 3.6 6.4 + - - +
141D GLN 3.6 1.4 + - - -
142D LYS* 2.9 61.8 + - + +
144D GLN 3.8 12.2 - - - +
145D LEU* 3.3 22.3 + - - +
146D LEU* 5.6 0.9 - - - -
147D SER 5.9 0.8 + - - -
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D LEU* 3.7 30.7 - - + -
110D VAL* 4.3 17.1 - - + +
113D SER* 4.2 7.2 - - - +
114D LYS* 3.5 47.1 - - + +
117D LEU* 3.8 15.5 - - + -
134D ALA 2.8 17.4 + - - +
135D LEU* 3.4 10.1 - - + +
137D ASN* 1.3 75.9 - - - +
139D ASN* 1.3 58.6 + - - +
140D LEU 3.0 0.4 - - - -
141D GLN* 2.7 30.7 + - - +
142D LYS 4.9 1.8 - - - +
145D LEU* 3.9 10.9 - - + +
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Residues in contact with ASN 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D LYS* 3.6 32.4 + - - +
135D LEU* 3.0 30.6 + - - +
136D ARG* 3.2 6.1 + - - +
138D LEU* 1.3 77.5 - - - +
140D LEU* 1.3 62.8 + - + +
141D GLN* 3.1 9.9 + - - +
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ARG* 2.9 28.8 + - + +
137D ASN* 4.0 9.0 - - - +
138D LEU 3.0 0.2 - - - -
139D ASN* 1.3 79.6 - - + +
141D GLN* 1.3 69.0 + - - +
142D LYS* 2.9 23.8 + - - +
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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