Contacts of the strand formed by residues 155 - 161 (chain H) in PDB entry 5D7I
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 155 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H PRO* 4.6 1.3 - - + -
150H PHE* 3.6 48.5 - - + -
153H ASP 3.6 4.2 + - - +
154H HIS* 1.3 83.7 + - - +
156H GLU* 1.3 70.5 + - - +
157H LEU 4.2 0.2 - - - -
176H PRO* 5.7 2.2 - - + -
190H LEU* 3.8 26.1 - - + +
212H VAL* 3.8 20.9 - - + -
213H GLN 3.1 11.7 - - - +
214H PHE* 4.0 13.9 - - + -
215H TYR* 4.8 0.2 - - - -
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Residues in contact with GLU 156 (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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154H HIS* 4.0 12.3 - - + -
155H VAL* 1.3 79.6 - - - +
157H LEU* 1.3 61.2 + - - +
158H SER* 5.1 0.9 + - - -
211H GLN* 3.6 2.3 + - - +
212H VAL* 3.5 2.3 - - - -
213H GLN* 2.8 45.5 + - + +
215H TYR* 3.0 35.9 + - + -
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Residues in contact with LEU 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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145H CYS* 4.0 7.2 - - + +
147H ALA* 4.9 5.6 - - + -
155H VAL 4.2 1.0 + - - -
156H GLU* 1.3 73.0 - - - +
158H SER* 1.3 74.6 + - - +
159H TRP* 3.9 11.0 - - + +
172H THR* 3.9 14.5 + - + +
190H LEU* 4.2 28.8 - - + +
191H SER 4.8 0.9 - - - -
192H SER* 3.5 40.4 - - - +
210H CYS* 3.7 26.2 - - - -
211H GLN 3.2 5.6 - - - +
212H VAL* 4.0 13.0 - - + +
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Residues in contact with SER 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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156H GLU 5.1 0.9 + - - -
157H LEU* 1.3 81.0 - - - +
159H TRP* 1.3 63.2 + - - +
160H TRP* 2.8 25.2 + - - -
165H GLU* 3.3 26.7 - - - -
210H CYS* 3.7 2.9 - - - -
211H GLN* 2.7 52.4 + - - +
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Residues in contact with TRP 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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127H VAL* 4.6 7.2 - - + -
143H LEU* 4.0 30.1 - - + -
144H VAL 4.1 1.8 - - - -
145H CYS* 3.5 42.6 - - + -
157H LEU* 3.9 8.2 - - + +
158H SER* 1.3 73.2 - - - +
160H TRP* 1.3 64.1 + - - +
161H VAL 4.2 0.2 - - - -
165H GLU* 3.2 10.0 - - - +
166H VAL* 3.0 47.4 + - + +
170H VAL* 3.7 28.2 - - + +
192H SER* 2.9 24.9 + - - -
193H ARG 3.8 4.9 + - - -
194H LEU* 3.5 40.4 - - + -
208H PHE* 4.9 3.6 - - + -
209H ARG 3.5 22.0 - - - -
210H CYS* 4.1 14.4 - - + -
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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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158H SER* 2.8 25.5 + - - -
159H TRP* 1.3 78.9 - - - +
161H VAL* 1.3 61.6 + - - +
162H ASN 4.1 0.2 + - - -
163H GLY* 3.6 22.3 + - - +
164H LYS* 3.4 10.8 - - - +
165H GLU* 3.3 46.0 - - + -
207H HIS* 3.6 3.8 + - - +
208H PHE* 3.6 0.5 - - - -
209H ARG* 2.8 71.9 + - + +
211H GLN* 3.5 40.6 - - + -
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Residues in contact with VAL 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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160H TRP* 1.3 77.6 - - - +
162H ASN* 1.3 82.8 + - - +
163H GLY 3.1 0.4 - - - -
164H LYS* 2.8 27.2 + - - +
166H VAL* 3.8 26.6 - - + +
194H LEU* 3.9 28.3 - - + -
196H VAL* 5.8 1.3 - - + -
200H PHE* 3.7 33.0 - - + -
207H HIS 3.3 8.5 - - - +
208H PHE* 4.0 11.4 - - + -
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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