Contacts of the helix formed by residues 134 - 143 (chain B) in PDB entry 5Y7G
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 ARG 134 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B LYS* 3.5 10.1 - - - +
133B LEU* 1.3 83.6 - - - +
135B LYS* 1.3 61.6 + - - +
136B ASP* 3.3 27.6 + - - +
137B ALA* 3.3 6.9 + - + +
138B LEU* 2.9 26.9 + - - +
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Residues in contact with LYS 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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112B PHE* 3.4 45.1 + - + -
113B GLY 5.3 0.6 + - - -
115B LEU 2.9 26.2 + - - -
116B LYS* 3.8 1.6 - - - +
117B LYS* 3.7 43.3 - - + +
120B LEU* 3.9 13.9 - - + -
134B ARG* 1.3 71.8 - - - +
136B ASP* 1.3 67.3 + - - +
137B ALA 3.1 1.1 - - - -
138B LEU* 3.4 4.7 + - - -
139B LEU* 3.0 19.4 + - - +
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Residues in contact with ASP 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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134B ARG* 3.3 39.0 + - - +
135B LYS* 1.3 73.0 + - - +
137B ALA* 1.3 62.7 + - - -
139B LEU* 3.4 10.2 + - - +
140B GLU* 3.0 31.3 + - - +
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Residues in contact with ALA 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 LEU* 3.3 23.8 - - + +
134B ARG* 3.6 15.3 - - + +
135B LYS 3.1 1.0 - - - -
136B ASP* 1.3 82.8 + - - +
138B LEU* 1.3 60.6 + - - +
139B LEU 3.2 0.2 - - - -
140B GLU* 3.2 9.3 + - - +
141B ARG* 2.9 30.0 + - - +
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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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112B PHE* 4.1 13.5 - - + -
117B LYS* 4.7 9.4 - - + -
121B SER* 6.0 4.5 - - - +
128B LEU* 4.2 33.0 - - + +
131B ALA 4.4 3.4 - - - +
132B ASN* 5.3 2.2 - - + -
133B LEU* 3.2 55.1 - - + +
134B ARG 2.9 14.8 + - - +
135B LYS* 3.8 6.7 - - - +
137B ALA* 1.3 75.4 - - - +
139B LEU* 1.3 57.0 + - - +
141B ARG* 3.5 1.4 + - + +
142B LEU* 2.8 43.2 + - + +
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Residues in contact with LEU 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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108B LEU* 3.7 23.8 - - + -
109B ALA* 4.1 24.0 - - + +
112B PHE* 3.4 42.7 - - + -
135B LYS 3.0 14.4 + - - +
136B ASP* 3.5 12.6 - - - +
137B ALA 3.2 0.2 - - - -
138B LEU* 1.3 76.2 - - - +
140B GLU* 1.3 58.4 + - - +
142B LEU* 3.6 1.1 - - - -
143B GLN* 2.8 42.3 + - + +
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Residues in contact with GLU 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 ASP* 3.0 17.8 + - - +
137B ALA* 3.2 10.6 + - - +
139B LEU* 1.3 77.0 - - - +
141B ARG* 1.3 57.5 + - - +
143B GLN* 4.1 4.9 - - - +
144B PRO* 3.2 22.5 - - - +
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Residues in contact with ARG 141 (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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128B LEU* 3.2 48.1 - - + +
130B ARG* 3.3 13.5 - - - +
131B ALA* 3.0 50.5 + - - +
133B LEU* 3.6 16.0 - - + +
137B ALA 2.9 16.1 + - - +
138B LEU* 4.1 2.7 - - - +
140B GLU* 1.3 77.5 - - - +
142B LEU* 1.3 58.0 + - - +
143B GLN 3.5 0.2 - - - -
144B PRO* 3.8 13.4 - - - +
145B LEU* 4.7 8.3 - - - +
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Residues in contact with LEU 142 (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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108B LEU* 3.3 17.3 - - + +
112B PHE* 3.7 22.7 - - + -
124B PHE* 3.3 52.7 - - + -
127B HIS* 4.5 14.1 - - + -
128B LEU* 4.1 11.0 - - + +
138B LEU* 2.8 31.2 + - + +
139B LEU* 3.9 0.7 - - - +
141B ARG* 1.3 76.9 - - - +
143B GLN* 1.3 64.6 + - - +
144B PRO 3.5 0.9 - - - -
145B LEU* 3.4 5.5 + - + +
146B PHE* 3.2 28.7 + - + -
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Residues in contact with GLN 143 (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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108B LEU* 3.5 28.8 - - - +
109B ALA* 4.2 13.0 + - - +
139B LEU* 2.8 24.8 + - + +
140B GLU* 4.1 4.9 - - - +
142B LEU* 1.3 73.1 - - - +
144B PRO* 1.3 71.7 - - + +
145B LEU 3.1 2.9 + - - -
146B PHE 3.4 1.9 + - - -
147B PRO* 3.3 28.6 + - + +
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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