Contacts of the helix formed by residues 130 - 138 (chain B) in PDB entry 4ZDH
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 130 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A TYR* 3.6 30.9 - - - +
123A GLN 3.8 18.8 + - - -
124A LEU* 3.9 8.6 - - - +
201A PRO* 5.6 0.2 - - - +
128B GLU 3.5 3.0 + - - -
129B PRO* 1.3 75.0 - - - +
131B GLU* 1.3 63.6 + - - +
132B ALA* 3.1 14.2 + - - +
133B GLU* 3.2 17.0 + - - +
134B ILE* 3.3 22.7 + - - +
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLU* 6.1 4.5 - - + -
129B PRO 3.7 2.2 + - - -
130B SER* 1.3 72.9 + - - +
132B ALA* 1.3 61.4 + - - +
134B ILE* 3.4 28.8 + - - +
135B SER* 3.1 25.1 + - - +
201B GLN* 5.2 3.7 + - - -
243B ASP 4.1 20.8 - - - +
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Residues in contact with ALA 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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122A TYR* 3.8 3.0 - - + -
199A PHE* 4.2 6.4 - - + -
201A PRO* 3.9 34.3 - - + -
130B SER* 3.1 8.5 + - - +
131B GLU* 1.3 77.4 - - - +
133B GLU* 1.3 60.1 + - - +
135B SER* 3.4 7.3 + - - -
136B HIS* 3.0 32.1 + - - +
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Residues in contact with GLU 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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122A TYR* 3.4 42.4 - - + +
124A LEU* 5.5 0.9 - - - +
136A LEU* 4.8 3.3 - - - +
138A THR* 5.0 0.3 - - - +
129B PRO* 4.4 0.3 - - - +
130B SER* 3.2 23.3 + - - +
131B GLU 3.3 0.2 - - - -
132B ALA* 1.3 76.5 - - - +
134B ILE* 1.3 56.2 + - - +
136B HIS 3.3 0.2 + - - -
137B THR* 2.8 42.4 + - - +
139B LYS 3.5 10.1 - - - +
140B ALA* 3.7 2.4 - - - -
141B THR* 2.7 53.0 + - - +
194B ARG* 3.0 22.5 + - - +
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Residues in contact with ILE 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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129B PRO* 4.2 7.4 - - + +
130B SER 3.3 16.2 + - - +
131B GLU* 3.6 28.5 - - - +
132B ALA 3.4 0.2 - - - -
133B GLU* 1.3 76.4 - - - +
135B SER* 1.3 58.4 + - - +
138B GLN* 2.8 30.3 + - - +
139B LYS 3.5 17.9 - - - +
140B ALA* 4.1 10.3 - - + -
197B ALA* 3.6 21.1 - - + -
200B TRP* 3.7 33.2 - - + +
201B GLN* 3.7 18.6 - - + +
243B ASP 5.5 1.1 - - - +
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Residues in contact with SER 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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131B GLU* 3.1 21.7 + - - +
132B ALA* 3.4 12.0 + - - -
134B ILE* 1.3 77.7 - - - +
136B HIS* 1.3 66.7 + - - +
138B GLN* 4.5 7.7 + - - +
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Residues in contact with HIS 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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118A ASP* 2.6 46.4 + - - +
122A TYR* 3.7 12.3 - - - +
199A PHE* 3.7 44.1 - + + +
132B ALA 3.0 19.5 + - - +
133B GLU 3.9 1.8 - - - +
135B SER* 1.3 80.2 + - - +
137B THR* 1.3 58.8 + - + +
138B GLN* 5.5 0.5 - - - +
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Residues in contact with THR 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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118A ASP* 3.9 14.6 - - - +
122A TYR* 3.8 18.8 - - - +
139A ASP* 3.8 19.5 - - - +
169A PHE* 6.5 0.2 - - - -
133B GLU* 2.8 26.6 + - + +
136B HIS* 1.3 76.2 - - + +
138B GLN* 1.3 70.9 + - - +
139B LYS* 3.0 44.9 + - - +
194B ARG* 3.8 7.5 + - - +
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Residues in contact with GLN 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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167A MET* 5.3 1.7 - - - +
134B ILE 2.8 27.2 + - - +
135B SER* 4.7 7.0 - - - +
136B HIS 5.4 0.7 - - - +
137B THR* 1.3 75.5 + - - +
139B LYS* 1.3 62.0 + - - +
196B SER* 3.9 4.5 - - - -
197B ALA* 3.0 27.8 + - + +
198B THR* 6.3 1.6 - - - +
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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