Contacts of the strand formed by residues 153 - 158 (chain B) in PDB entry 3S3O
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 THR 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B VAL* 4.4 0.4 - - + -
145B VAL 3.2 9.9 - - - +
146B VAL* 3.8 4.6 - - + +
151B GLY 3.5 12.0 + - - -
152B PHE* 1.3 79.0 - - - +
154B TRP* 1.3 65.2 + - - +
155B LEU* 3.6 31.0 - - + -
223B LYS* 3.6 21.7 - - - +
227B ILE* 4.0 15.3 - - + +
250B GLN* 3.3 9.2 - - + +
253B LEU* 4.3 14.4 - - + +
254B ASN* 2.7 34.9 + - - -
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Residues in contact with TRP 154 (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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176A ILE* 3.5 36.1 - - + +
270A PHE* 5.9 2.2 - + - -
122B PHE* 4.9 10.3 - + - -
125B PHE* 3.8 34.8 - + - -
143B LEU 3.9 0.9 - - - +
144B VAL* 3.7 0.2 - - - -
145B VAL* 2.8 53.0 + - + +
147B ASP* 4.1 9.2 - - + -
152B PHE* 3.8 40.5 - + + -
153B THR* 1.3 76.7 - - - +
155B LEU* 1.3 64.3 + - - +
156B TYR* 3.8 25.4 - - + -
173B LEU* 3.5 25.7 - - + +
176B ILE* 5.6 9.7 - - + +
177B ALA* 5.5 3.8 - - + -
250B GLN* 3.2 5.2 - - - -
269B LEU* 4.3 15.3 - - + -
394B HEZ 4.0 2.9 - - - +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B VAL* 3.9 13.0 - - + -
143B LEU 3.5 1.8 - - - -
144B VAL* 4.0 26.2 - - + -
153B THR* 3.6 21.5 - - + -
154B TRP* 1.3 74.8 - - - +
156B TYR* 1.3 64.7 + - - +
157B PRO* 4.3 1.1 - - - +
227B ILE* 4.6 11.4 - - + -
231B LEU* 5.7 2.0 - - + -
246B LEU* 4.0 26.0 - - + +
249B VAL* 3.8 30.3 - - + -
250B GLN* 3.3 29.0 + - + +
253B LEU* 4.4 3.6 - - + -
394B HEZ 2.8 34.7 + - - +
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Residues in contact with TYR 156 (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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172A VAL* 6.3 0.4 - - + -
142B VAL* 3.4 4.9 - - - +
143B LEU* 2.7 47.2 + - + +
145B VAL* 4.4 14.1 - - + -
154B TRP* 3.8 21.8 - - + -
155B LEU* 1.3 77.8 - - - +
157B PRO* 1.3 70.9 - - + +
158B THR* 3.6 0.9 + - - +
169B SER* 3.6 37.9 - - - +
170B LEU* 5.3 0.4 - - + -
172B VAL* 4.2 22.4 - - + +
173B LEU* 3.3 45.5 + - + +
176B ILE* 5.7 2.3 - - - +
394B HEZ 3.3 31.6 + - + -
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Residues in contact with PRO 157 (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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139B TYR* 3.7 33.6 - - + -
141B TYR 3.3 8.7 - - - +
142B VAL* 4.5 0.7 - - - -
156B TYR* 1.3 87.0 - - + +
158B THR* 1.3 61.8 - - - +
169B SER* 4.4 3.8 + - - -
242B TRP* 4.3 3.4 - - + -
243B TYR* 3.7 25.8 - - + -
246B LEU* 3.9 27.1 - - + -
394B HEZ 4.1 16.8 - - + -
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Residues in contact with THR 158 (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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129B TYR* 3.5 23.7 - - + +
139B TYR* 3.6 10.8 - - - -
140B LEU 3.0 22.5 + - - -
141B TYR* 2.9 32.3 + - - +
143B LEU* 4.5 1.8 - - + -
156B TYR 3.9 7.2 - - - +
157B PRO* 1.3 79.8 - - - +
159B LYS* 1.3 60.3 + - - +
160B ALA 3.0 20.5 + - - -
165B ALA* 3.8 13.0 - - + +
169B SER* 3.6 20.4 - - - +
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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