Contacts of the strand formed by residues 154 - 161 (chain D) in PDB entry 4F9P
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 154 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149D VAL* 5.1 0.3 - - - +
153D ASP* 1.3 79.7 + - - +
155D VAL* 1.3 69.1 + - - +
156D SER* 5.3 0.7 - - - -
211D ILE 3.6 13.7 - - - -
212D ASN* 4.6 12.1 - - - -
213D SER 4.8 0.2 - - - -
214D VAL* 4.7 0.7 - - - -
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Residues in contact with VAL 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D LEU* 4.1 20.4 - - + -
148D SER 5.5 0.4 - - - +
149D VAL* 3.6 33.2 - - + -
154D SER* 1.3 77.8 - - - +
156D SER* 1.3 68.4 + - - +
157D LEU* 3.9 29.2 - - + -
209D LEU 3.8 0.3 - - - +
210D SER* 3.6 1.7 - - - -
211D ILE* 3.1 49.0 + - + +
214D VAL* 4.5 4.0 - - + -
240D LEU* 4.9 11.7 - - + -
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Residues in contact with SER 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D SER 5.1 1.2 - - - +
144D PRO* 5.7 1.6 - - - +
147D LEU* 5.1 6.2 - - - +
154D SER* 5.3 1.0 - - - -
155D VAL* 1.3 79.7 + - - +
157D LEU* 1.3 65.2 + - - +
158D SER* 4.1 1.7 + - - -
208D THR* 3.9 20.4 - - - -
209D LEU 3.2 4.9 - - - -
210D SER* 4.2 7.9 + - - -
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D SER 4.4 2.5 - - - +
147D LEU* 3.6 30.5 - - + -
155D VAL* 3.9 19.3 - - + -
156D SER* 1.3 73.5 - - - +
158D SER* 1.3 60.5 + - - +
171D TRP* 4.2 9.5 - - + -
207D PHE 3.7 0.2 - - - +
208D THR* 3.1 9.0 - - - +
209D LEU* 2.7 56.4 + - + +
211D ILE* 5.5 3.6 - - + -
222D TYR* 3.7 41.3 - - + -
238D THR* 3.7 20.2 - - + +
240D LEU* 5.8 8.3 - - + -
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Residues in contact with SER 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D GLN* 3.5 8.0 - - - +
143D SER* 2.8 53.0 + - - +
156D SER 4.1 1.7 + - - -
157D LEU* 1.3 74.2 - - - +
159D CYS* 1.3 62.3 + - - +
160D ARG* 4.2 1.3 - - - -
171D TRP* 4.1 2.5 - - - -
206D GLU* 5.5 6.1 - - - -
207D PHE 3.4 7.0 - - - -
208D THR* 4.7 3.8 - - - +
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Residues in contact with CYS 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D LEU* 3.8 18.6 - - - -
141D THR 3.5 5.6 - - - -
142D GLN* 4.4 1.8 - - - +
158D SER* 1.3 72.7 - - - +
160D ARG* 1.3 61.1 + - - +
161D ALA* 3.9 1.1 + - - -
169D LEU* 4.9 6.3 - - + -
171D TRP* 3.3 22.8 - - + -
205D THR 3.5 4.0 - - - +
206D GLU* 5.0 1.8 - - - -
207D PHE* 3.0 36.6 + - + +
224D CYS* 2.1 48.9 - - + -
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Residues in contact with ARG 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D VAL 3.6 1.2 - - - +
140D LEU* 3.4 2.6 - - - -
141D THR* 2.8 54.7 + - - +
143D SER* 6.6 0.2 - - - -
158D SER* 4.2 0.8 - - - -
159D CYS* 1.3 73.8 - - - +
161D ALA* 1.3 62.8 + - - +
205D THR 3.7 4.0 - - - -
206D GLU* 3.5 26.7 - - - +
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Residues in contact with ALA 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D ILE* 5.8 3.8 - - + -
139D VAL 3.8 5.2 - - - +
140D LEU* 4.5 6.5 - - + +
159D CYS* 3.9 1.9 + - - -
160D ARG* 1.3 75.8 - - - +
162D SER* 1.3 69.7 + - - +
163D GLN 3.7 11.4 - - - +
165D ILE* 3.5 33.7 - - + -
205D THR* 3.0 31.3 + - - +
207D PHE* 4.9 0.9 - - + -
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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