Contacts of the strand formed by residues 149 - 155 (chain F) in PDB entry 3ZWG
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 TRP 149 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148F GLY* 1.3 72.2 - - - -
150F HIS* 1.3 67.8 + - - +
151F SER* 4.4 1.7 + - - +
161F ARG* 3.4 42.6 - - + -
162F GLY* 3.3 43.3 - - - -
163F PHE* 3.6 34.9 - + + -
173F GLU* 3.9 33.4 - - + -
175F HIS* 4.5 1.3 - + - -
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Residues in contact with HIS 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F TRP* 3.7 14.8 - + + -
143F PHE* 3.2 52.0 - + + +
144F ARG 4.0 5.5 + - - -
146F ASP* 2.8 38.6 + - - -
148F GLY 3.2 20.5 + - - -
149F TRP* 1.3 80.1 + - - +
151F SER* 1.3 63.8 + - - +
152F ARG 4.3 0.2 + - - -
160F SER 3.6 1.4 - - - +
161F ARG* 3.5 1.8 - - - -
162F GLY 2.9 32.5 + - - -
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Residues in contact with SER 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F PHE* 4.6 3.6 - - - -
149F TRP* 4.3 2.1 - - - +
150F HIS* 1.3 76.7 + - - +
152F ARG* 1.3 63.2 + - - +
159F LYS* 5.3 12.1 - - - -
160F SER 3.1 9.4 - - - -
161F ARG* 3.7 22.9 - - - +
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Residues in contact with ARG 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F ASN* 3.4 14.6 + - - -
119F VAL 4.1 7.6 + - - -
120F ARG* 2.5 47.2 - - - +
140F ARG 3.8 1.9 + - - -
141F SER* 2.8 28.6 + - - -
143F PHE* 3.4 43.8 - - + -
150F HIS 4.2 0.2 - - - -
151F SER* 1.3 76.0 - - - +
153F GLY* 1.3 75.6 + - - +
154F LEU* 3.6 2.4 + - - +
159F LYS* 4.3 4.2 - - - +
160F SER* 2.9 36.4 + - - +
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Residues in contact with GLY 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F ARG* 4.8 4.3 + - - -
152F ARG* 1.3 90.8 - - - +
154F LEU* 1.3 61.6 + - - +
155F GLY 3.5 2.7 - - - -
158F LEU 3.9 1.1 - - - -
159F LYS* 3.8 14.9 - - - +
179F ALA* 6.1 0.7 - - - -
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Residues in contact with LEU 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F LEU* 4.0 15.3 - - + -
119F VAL* 3.3 38.4 - - + +
120F ARG* 3.9 16.4 + - - +
121F VAL* 3.6 31.8 + - + +
152F ARG* 4.4 2.9 - - - +
153F GLY* 1.3 76.6 - - - +
155F GLY* 1.3 61.2 + - - +
156F TYR* 3.6 14.2 - - - -
158F LEU* 2.9 23.0 + - + +
159F LYS* 4.1 9.0 - - - -
160F SER* 3.8 28.9 - - - +
176F VAL* 4.2 7.0 - - + -
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Residues in contact with GLY 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F GLY* 3.5 3.2 - - - -
154F LEU* 1.3 80.5 - - - +
156F TYR* 1.3 63.1 + - - +
157F GLY 2.8 16.9 + - - -
158F LEU* 2.8 19.5 + - - +
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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