Contacts of the strand formed by residues 171 - 177 (chain B) in PDB entry 4H3E
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 LEU 171 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B PHE* 4.6 3.8 - - + -
131B ALA* 3.7 41.5 - - + +
132B VAL* 4.0 16.6 - - + +
135B GLN* 3.2 28.2 + - + +
136B PHE* 3.9 20.5 - - + -
161B LEU* 3.9 20.9 - - + -
162B CYS 3.2 13.2 - - - +
163B VAL* 4.1 7.4 - - + -
169B ASN 3.5 2.0 + - - +
170B GLN* 1.3 75.2 - - - +
172B VAL* 1.3 60.9 + - - +
190B VAL* 4.4 4.9 - - + -
228B HIS* 3.8 27.4 - - + +
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Residues in contact with VAL 172 (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 PHE* 4.7 2.0 - - - -
161B LEU* 3.5 6.7 - - - +
162B CYS* 2.7 51.9 + - + +
164B ASP* 4.5 11.7 - - + +
170B GLN* 4.5 3.4 - - + +
171B LEU* 1.3 77.1 - - - +
173B ILE* 1.3 73.3 + - - +
174B ASP* 3.9 1.1 + - + -
187B LEU* 4.2 25.1 - - + -
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Residues in contact with ILE 173 (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 PHE* 4.0 22.3 - - + -
142B PHE* 4.1 17.9 - - + -
145B ALA* 3.8 17.3 - - + +
146B PHE* 3.6 34.1 - - + +
149B ALA* 3.8 27.6 - - + -
159B THR* 4.2 9.4 - - + -
160B TRP 3.2 13.0 - - - +
161B LEU* 4.3 1.3 - - + -
172B VAL* 1.3 85.2 - - - +
174B ASP* 1.3 65.0 + - - +
175B ASN 5.3 0.2 - - - +
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Residues in contact with ASP 174 (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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159B THR* 3.7 0.2 - - - -
160B TRP* 2.8 49.9 + - + +
162B CYS* 4.5 5.4 - - - -
172B VAL* 3.9 2.0 + - + +
173B ILE* 1.3 78.3 - - - +
175B ASN* 1.3 66.7 + - - +
176B THR* 3.7 11.6 - - - +
182B PRO* 4.6 6.2 - - - +
185B LYS* 2.9 41.4 + - - +
187B LEU* 4.0 21.4 - - + +
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Residues in contact with ASN 175 (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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149B ALA* 2.9 33.3 + - - +
152B ASN* 4.6 3.0 + - - +
153B ASN* 3.6 28.5 + - - +
158B TRP 3.6 1.8 - - - -
159B THR* 2.8 31.9 + - - +
174B ASP* 1.3 80.4 + - - +
176B THR* 1.3 64.8 + - - +
185B LYS* 4.4 3.3 + - - -
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Residues in contact with THR 176 (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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153B ASN* 3.3 12.4 + - - +
157B GLY* 3.3 1.6 - - - -
158B TRP* 2.9 37.8 + - - +
160B TRP* 2.9 23.3 + - - +
174B ASP* 3.7 14.3 + - - +
175B ASN* 1.3 78.2 - - - +
177B SER* 1.3 59.6 + - - +
180B GLY* 2.7 40.5 + - - +
181B CYS 4.1 2.5 - - - +
182B PRO* 4.4 5.6 - - + -
185B LYS* 3.9 11.4 - - - +
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Residues in contact with SER 177 (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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178A ASN* 4.5 12.1 + - - -
153B ASN* 5.1 2.7 - - - -
154B PHE 5.1 4.3 + - - -
156B SER 3.6 8.9 + - - -
176B THR* 1.3 74.2 - - - +
178B ASN* 1.3 79.1 + - - +
179B ALA 3.1 0.5 + - - -
180B GLY* 2.9 21.8 + - - -
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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