Contacts of the strand formed by residues 141 - 147 (chain B) in PDB entry 3ZXR
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 141 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B PHE* 3.6 4.1 - - - +
140B ASP* 1.3 83.4 - - - +
142B VAL* 1.3 64.1 + - - +
154B GLU* 4.5 4.0 + - - -
155B VAL* 3.4 4.5 - - - +
156B ASP* 2.9 45.2 + - - +
259B THR* 3.7 6.9 - - - +
167C ALA 6.1 0.4 - - - -
174C PRO* 3.8 17.3 - - - -
175C ASN* 3.2 16.4 - - - -
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B PHE* 5.7 2.2 - - + -
141B SER* 1.3 77.1 - - - +
143B SER* 1.3 65.2 + - - +
144B PHE* 4.0 23.1 - - + -
153B TYR* 6.0 2.2 - - + -
154B GLU 3.3 13.2 - - - +
155B VAL* 3.9 17.5 - - + -
259B THR* 4.6 7.0 - - + +
175C ASN* 2.8 33.4 + - - +
176C ARG* 3.7 6.1 - - - +
177C GLY* 3.5 28.3 + - - +
178C TYR* 6.3 0.2 - - + -
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Residues in contact with SER 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B VAL* 1.3 77.2 - - - +
144B PHE* 1.3 69.4 + - - +
152B PHE* 3.5 20.4 - - - -
153B TYR* 3.2 1.7 - - - +
154B GLU* 2.9 38.8 + - - +
164C THR 3.1 15.3 - - - -
165C GLY 4.1 0.2 - - - -
166C ALA 3.5 22.6 + - - -
167C ALA* 4.9 4.7 + - - -
175C ASN* 3.6 2.0 - - - -
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Residues in contact with PHE 144 (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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142B VAL* 4.0 24.0 - - + -
143B SER* 1.3 80.9 - - - +
145B ASP* 1.3 58.6 + - - +
152B PHE* 3.1 21.0 - - - +
153B TYR* 3.8 11.2 - - + -
161C TRP* 3.8 26.0 - + - -
164C THR* 2.7 72.1 + - + -
165C GLY* 3.1 4.1 + - - -
177C GLY* 5.3 8.7 - - - -
178C TYR 6.1 0.7 - - - -
179C LYS 6.4 0.4 - - - -
181C ARG* 6.3 0.2 - - - -
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Residues in contact with ASP 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PHE* 1.3 80.2 - - - +
146B SER* 1.3 55.2 + - - +
147B ARG* 2.7 48.8 + - + -
151B SER* 2.6 26.9 + - - -
152B PHE* 3.1 32.9 + - - +
164C THR* 4.3 6.3 - - - +
165C GLY* 4.3 9.7 - - - +
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Residues in contact with SER 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ASP* 1.3 79.9 - - - +
147B ARG* 1.3 66.1 + - - +
150B GLY 4.1 0.9 - - - -
151B SER* 3.7 13.2 + - - -
466B ARG* 3.1 37.4 + - - +
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Residues in contact with ARG 147 (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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145B ASP* 2.7 42.7 + - + +
146B SER* 1.3 80.6 + - - +
148B ALA* 1.3 67.5 + - - +
149B ASN* 3.3 32.7 + - - +
150B GLY* 2.9 40.2 + - - +
151B SER* 3.7 5.7 - - - +
152B PHE* 4.6 5.1 - - - -
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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