Contacts of the strand formed by residues 156 - 162 (chain H) in PDB entry 5U2V
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 VAL 156 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H PHE* 4.9 3.7 - - - -
124H PRO* 4.6 1.3 - - + -
148H ALA* 6.1 0.2 - - + -
151H PHE* 3.7 50.3 - - + -
154H ASP* 3.8 10.3 + - - +
155H HIS* 1.3 79.0 - - - +
157H GLU* 1.3 70.9 + - - +
177H PRO* 4.7 2.2 - - + -
191H LEU* 4.2 20.4 - - + -
213H VAL* 3.8 24.2 - - + -
214H GLN 3.2 7.6 - - - +
215H PHE* 4.1 10.1 - - + -
216H TYR* 5.0 0.7 - - - -
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Residues in contact with GLU 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H LYS* 4.1 15.1 + - - +
10H PHE* 3.8 19.0 - - + -
156H VAL* 1.3 80.8 - - - +
158H LEU* 1.3 62.3 + - - +
159H SER* 4.0 2.0 + - - -
212H GLN* 3.7 1.9 + - - +
213H VAL* 3.6 2.7 - - - -
214H GLN* 3.1 37.0 + - + +
216H TYR* 3.2 30.9 + - + -
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Residues in contact with LEU 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H CYS* 4.1 7.0 - - + -
148H ALA* 4.8 2.5 - - + -
156H VAL 4.2 0.6 - - - -
157H GLU* 1.3 74.7 - - - +
159H SER* 1.3 74.3 + - - +
160H TRP* 4.0 7.4 - - + +
173H THR* 3.9 14.7 + - + +
191H LEU* 4.0 39.4 - - + +
193H SER* 3.5 36.8 - - - +
211H CYS* 3.9 25.8 - - - -
212H GLN 3.4 3.1 - - - -
213H VAL* 4.0 17.9 - - + +
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Residues in contact with SER 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H GLU 4.9 2.3 + - - -
158H LEU* 1.3 80.2 - - - +
160H TRP* 1.3 64.3 + - - +
161H TRP* 2.9 25.5 + - - -
166H GLU* 3.3 24.2 - - - -
211H CYS* 3.8 2.9 - - - -
212H GLN* 2.8 50.4 + - - +
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Residues in contact with TRP 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H VAL* 4.5 7.9 - - + -
144H LEU* 3.8 33.4 - - + -
145H VAL 4.2 1.6 - - - -
146H CYS* 3.5 39.0 - - + -
158H LEU* 4.0 4.9 - - + +
159H SER* 1.3 77.8 - - - +
161H TRP* 1.3 64.0 + - - +
166H GLU* 3.1 10.8 + - - +
167H VAL* 2.9 47.0 + - + +
171H VAL* 3.7 28.5 - - + +
173H THR* 4.9 0.2 - - - -
193H SER* 2.9 22.7 + - - -
194H ARG 3.8 6.7 + - - -
195H LEU* 3.6 40.4 - - + -
209H PHE* 5.0 3.8 - - + -
210H ARG 3.7 15.7 - - - -
211H CYS* 4.1 14.4 - - + -
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Residues in contact with TRP 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H SER* 2.9 26.6 + - - -
160H TRP* 1.3 81.7 + - - +
162H VAL* 1.3 62.2 + - - +
163H ASN 4.1 0.4 + - - -
164H GLY* 3.6 26.0 - - - +
165H LYS* 3.2 6.5 - - - +
166H GLU* 3.5 39.5 - - + -
208H HIS* 3.6 2.7 + - + +
209H PHE* 3.5 2.9 - - - -
210H ARG* 2.8 70.5 + - + +
212H GLN* 3.6 36.9 - - + +
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Residues in contact with VAL 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161H TRP* 1.3 75.4 - - - +
163H ASN* 1.3 84.0 + - - +
165H LYS* 2.6 24.8 + - - +
167H VAL* 3.7 34.3 - - + +
195H LEU* 3.8 9.2 - - + -
197H VAL* 5.8 1.3 - - + -
201H PHE* 3.8 31.0 - - + -
207H ASN* 4.6 0.2 - - - +
208H HIS 3.1 9.4 - - - +
209H PHE* 3.8 24.5 - - + -
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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