Contacts of the helix formed by residues 127 - 140 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B ALA* 3.6 9.3 - - + +
95B PHE 5.6 0.2 - - - +
125B ALA 4.1 0.2 - - - -
126B VAL* 1.3 89.0 - - + +
128B LEU* 1.3 65.7 + - - +
129B GLU* 4.4 8.3 - - + +
130B MET* 3.3 49.3 + - + +
131B LEU 3.8 0.9 + - - -
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B VAL* 4.1 37.5 - - + +
125B ALA 4.1 9.2 + - - +
126B VAL* 3.9 7.3 - - + +
127B PRO* 1.3 71.7 - - - +
129B GLU* 1.3 63.6 + - - +
131B LEU* 3.0 9.5 + - + +
132B GLU* 3.0 43.7 + - + +
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Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B PRO* 3.2 7.5 - - + +
128B LEU* 1.3 77.9 - - - +
130B MET* 1.3 64.3 + - - +
132B GLU* 3.1 26.2 + - - +
133B ILE* 2.9 41.2 + - + +
136B ARG* 4.1 15.1 + - - -
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Residues in contact with MET 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ALA* 4.3 2.5 - - + -
95B PHE* 3.8 32.5 - - + -
98B ILE* 3.4 22.6 - - + +
127B PRO* 3.3 38.1 + - + +
128B LEU 3.2 0.6 - - - -
129B GLU* 1.3 80.6 - - - +
131B LEU* 1.3 57.3 + - - +
133B ILE* 3.5 10.9 + - + +
134B ALA* 3.1 26.7 + - - +
146B LEU* 3.6 24.1 - - + +
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ALA* 3.7 17.3 - - + +
97B HIS* 4.6 0.7 - - + -
98B ILE* 3.7 27.4 - - + -
117B LEU* 4.2 12.4 - - + +
120B ALA* 3.6 24.5 - - + -
121B VAL* 3.8 40.6 - - + +
125B ALA* 3.6 27.6 - - + +
127B PRO 4.3 1.6 - - - +
128B LEU* 3.0 12.7 + - + +
130B MET* 1.3 73.4 - - - +
132B GLU* 1.3 64.6 + - - +
134B ALA* 3.4 2.9 + - - +
135B LEU* 3.0 31.2 + - + +
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B VAL* 5.7 1.6 - - + -
128B LEU* 3.0 45.4 + - + +
129B GLU* 3.1 29.1 + - - +
131B LEU* 1.3 78.3 - - - +
133B ILE* 1.3 61.2 + - - +
135B LEU* 3.5 11.0 + - + +
136B ARG* 3.1 44.7 + - - +
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Residues in contact with ILE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B GLU* 2.9 35.6 + - + +
130B MET* 3.7 8.7 - - + +
132B GLU* 1.3 75.8 - - - +
134B ALA* 1.3 63.9 + - - +
136B ARG* 3.4 26.0 + - - +
137B ASN* 3.1 37.0 + - - +
146B LEU* 3.6 20.6 - - + -
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ILE* 4.1 11.0 - - + -
117B LEU* 3.9 26.9 - - + -
130B MET 3.1 17.9 + - - +
131B LEU 3.7 4.9 - - - +
132B GLU 3.3 0.2 - - - -
133B ILE* 1.3 77.7 - - - +
135B LEU* 1.3 56.3 + - - +
137B ASN* 3.5 0.9 + - - +
138B LEU* 3.0 22.5 + - - +
145B LEU* 3.4 37.9 - - + +
146B LEU* 4.1 1.8 - - + +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LYS* 4.3 17.3 - - + -
117B LEU* 3.8 31.2 - - + -
118B GLN* 3.9 26.9 - - + +
121B VAL* 4.1 23.8 - - + -
131B LEU 3.0 21.3 + - - +
132B GLU* 3.7 8.7 - - + +
134B ALA* 1.3 73.7 - - - +
136B ARG* 1.3 59.7 + - + +
138B LEU* 3.2 5.8 + - + +
139B ASN* 2.8 30.5 + - - +
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Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B GLU* 4.1 10.5 + - - -
132B GLU* 3.1 35.3 + - - +
133B ILE* 3.4 33.9 + - - +
135B LEU* 1.3 74.5 - - - +
137B ASN* 1.3 61.3 + - - +
139B ASN* 3.1 9.0 + - - +
140B LEU* 2.9 36.3 + - + +
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ILE* 3.1 28.1 + - - +
134B ALA 3.8 1.8 - - - +
136B ARG* 1.3 75.6 - - - +
138B LEU* 1.3 63.2 + - - +
140B LEU* 3.2 12.2 + - - +
142B LYS* 3.0 61.6 + - + +
144B GLN 3.9 12.9 + - - +
145B LEU* 2.7 33.6 + - - +
146B LEU* 4.4 3.4 - - - +
147B SER* 5.0 4.4 + - - +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LEU* 3.8 31.0 - - + -
110B VAL* 4.2 17.9 - - + +
113B SER* 4.2 4.9 - - - +
114B LYS* 3.5 49.8 - - + +
117B LEU* 4.1 11.7 - - + -
134B ALA 3.0 14.5 + - - +
135B LEU* 3.4 11.2 - - + +
137B ASN* 1.3 76.8 - - - +
139B ASN* 1.3 54.0 + - - +
140B LEU 3.1 0.2 - - - -
141B GLN* 2.7 30.9 + - - +
142B LYS 4.8 4.3 - - - +
145B LEU* 3.8 15.9 - - + +
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Residues in contact with ASN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LYS* 5.3 10.5 + - - -
135B LEU 2.8 16.6 + - - +
136B ARG* 3.1 7.9 + - - +
138B LEU* 1.3 72.1 - - - +
140B LEU* 1.3 62.0 + - - +
141B GLN* 2.9 28.9 + - - +
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ARG* 2.9 20.4 + - + +
137B ASN* 3.5 14.1 - - - +
138B LEU 3.1 0.6 - - - -
139B ASN* 1.3 82.2 - - - +
141B GLN* 1.3 76.1 - - - +
142B LYS* 3.1 35.1 + - + +
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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