Contacts of the strand formed by residues 188 - 197 (chain J) in PDB entry 5HHM
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 TYR 188 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148J THR 3.4 0.9 - - - -
149J GLY 2.9 29.3 + - - -
150J PHE* 2.6 47.7 + - + +
151J TYR* 3.8 18.8 - + - -
153J ASP* 3.6 36.3 + - + -
176J PRO* 3.7 23.3 - - + -
177J LEU 3.2 17.3 - - - -
178J LYS* 3.9 33.2 - - + -
179J GLU* 3.4 3.4 - - - +
184J ASN 5.6 1.2 + - - -
186J SER 3.4 17.9 + - - -
187J ARG* 1.3 73.8 - - - +
189J SER* 1.3 59.0 + - - +
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Residues in contact with SER 189 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154I TYR* 5.7 0.9 - - - -
176I TRP* 3.3 27.0 + - - -
147J ALA 3.1 5.8 - - - -
148J THR* 3.2 16.6 - - - +
150J PHE* 4.0 1.8 - - - -
176J PRO* 3.3 6.9 - - - +
177J LEU* 2.9 41.9 + - - +
179J GLU* 2.9 26.4 + - - +
188J TYR* 1.3 71.3 - - - +
190J LEU* 1.3 61.3 + - - +
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Residues in contact with LEU 190 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176I TRP* 5.4 0.9 - - - -
145J CYS 4.5 0.2 - - - -
146J LEU* 3.5 5.1 - - - +
147J ALA* 2.6 43.6 + - + +
150J PHE* 4.0 15.5 - - + -
155J VAL* 4.2 20.9 - - + +
157J LEU* 3.8 31.9 - - + +
172J THR* 3.9 11.9 - - + -
173J ASP* 3.8 35.7 - - + +
174J PRO 5.4 0.2 - - - -
175J GLN 4.4 0.4 - - - -
176J PRO* 4.1 21.5 - - + -
177J LEU* 5.9 0.4 - - - -
189J SER* 1.3 74.5 - - - +
191J SER* 1.3 64.8 + - - +
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Residues in contact with SER 191 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156I THR* 3.4 18.5 - - - +
174I VAL* 3.7 15.8 - - - +
176I TRP* 4.5 1.0 - - - -
145J CYS 3.2 12.6 - - - -
146J LEU* 4.1 12.6 - - - -
157J LEU* 5.2 0.2 - - - -
172J THR* 3.9 3.1 - - - +
173J ASP* 2.6 52.6 + - - +
177J LEU* 6.2 0.4 - - - +
190J LEU* 1.3 75.7 - - - +
192J SER* 1.3 61.0 - - - +
193J ARG* 3.2 14.2 + - - -
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Residues in contact with SER 192 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144J VAL* 3.6 2.8 - - - +
145J CYS* 2.8 35.0 + - - +
157J LEU* 3.6 23.1 - - - -
159J TRP* 3.0 25.2 + - - -
170J VAL* 4.2 0.2 - - - +
171J SER 3.6 6.6 - - - -
172J THR* 2.6 31.1 + - - -
191J SER* 1.3 75.1 - - - +
193J ARG* 1.3 69.0 + - - +
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Residues in contact with ARG 193 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135I LEU* 4.2 16.2 - - + -
156I THR* 3.9 3.6 + - - -
157I ASP 4.2 0.2 + - - -
159I THR* 3.3 22.5 + - - +
161I LEU* 4.0 15.9 - - + -
172I SER* 3.2 48.8 + - - -
173I ALA* 3.6 5.3 - - - +
174I VAL* 3.5 24.1 - - + +
142J THR* 4.1 9.2 - - + -
143J LEU 3.6 4.3 - - - -
144J VAL* 4.5 3.1 - - + -
159J TRP* 3.6 7.3 + - - -
169J GLY 4.0 1.3 - - - -
170J VAL* 3.2 6.8 - - - -
171J SER* 3.0 38.9 + - - +
173J ASP* 3.0 38.6 + - - -
191J SER* 3.2 15.8 + - - -
192J SER* 1.3 81.2 + - - +
194J LEU* 1.3 59.6 + - - +
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Residues in contact with LEU 194 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161I LEU* 4.4 0.4 - - - -
141J ALA 3.5 1.7 - - - +
142J THR* 3.3 2.6 - - - -
143J LEU* 2.7 45.2 + - + +
159J TRP* 3.7 48.2 - - + +
161J VAL* 3.8 26.2 - - + -
166J VAL* 4.3 6.3 - - + -
168J SER 3.9 16.2 - - - +
169J GLY 3.2 9.9 - - - +
170J VAL* 3.9 7.2 - - + -
193J ARG* 1.3 72.5 - - - +
195J ARG* 1.3 63.5 + - - +
196J VAL* 4.0 20.4 - - + -
208J PHE* 4.4 11.7 - - + -
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Residues in contact with ARG 195 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I TYR* 5.0 0.2 - - - -
137I THR* 3.5 24.1 + - - +
138I ASP* 2.8 42.2 + - - -
161I LEU* 3.6 22.0 - - + -
163I MET* 3.9 31.9 - - - +
168I PHE* 3.8 6.4 - - - -
170I SER* 3.3 26.1 + - - -
134J GLU* 3.2 21.2 + - - +
138J THR* 4.2 7.5 + - - +
140J LYS* 3.8 18.5 - - + +
141J ALA 3.2 7.9 - - - +
142J THR* 2.8 21.5 + - - +
168J SER 5.0 0.5 - - - +
169J GLY* 2.9 13.6 + - - -
194J LEU* 1.3 72.8 - - - +
196J VAL* 1.3 69.1 + - - +
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Residues in contact with VAL 196 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163I MET* 4.4 8.5 - - - -
140J LYS* 3.5 1.7 - - - -
141J ALA* 2.6 46.9 + - + +
143J LEU* 4.2 10.8 - - + -
161J VAL* 5.7 2.2 - - + -
194J LEU* 4.0 22.2 - - + -
195J ARG* 1.3 79.9 - - - +
197J SER* 1.4 68.0 + - - +
200J PHE* 4.3 23.6 - - + -
201J TRP* 4.1 23.1 - - + +
208J PHE* 4.4 8.1 - - + -
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Residues in contact with SER 197 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163I MET* 4.5 4.2 - - - +
166I MET* 3.9 26.2 - - - -
139J GLN 3.7 9.2 - - - -
140J LYS* 4.5 1.8 - - - +
196J VAL* 1.4 73.8 - - - +
198J ALA* 1.4 56.7 + - - +
199J THR* 3.2 22.3 + - - -
200J PHE* 2.8 35.6 + - - +
201J TRP 3.3 6.1 + - - -
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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