Contacts of the strand formed by residues 178 - 187 (chain H) in PDB entry 3IU3
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 178 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112H THR* 3.7 21.4 + - + +
146H ASP* 3.0 23.9 + - - -
147H TYR* 2.8 50.6 + - + +
148H PHE* 3.6 27.5 - + - -
149H PRO 4.4 3.8 - - - -
150H GLU* 3.8 41.7 - - + -
170H ALA* 4.2 8.7 - - + -
171H VAL 3.5 2.2 - - - -
172H LEU* 3.6 45.4 - - + +
173H GLN* 4.5 0.2 - - - -
177H LEU* 1.3 74.5 - - - +
179H SER* 1.3 61.4 + - - +
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Residues in contact with SER 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143H LEU* 4.1 10.4 - - - +
144H VAL 3.2 17.1 + - - -
145H LYS* 3.3 20.5 + - - +
147H TYR* 3.9 2.0 - - - -
169H PRO 4.6 0.3 - - - +
170H ALA* 4.6 0.4 - - - -
171H VAL* 2.9 36.3 + - - +
173H GLN* 3.1 27.6 - - - -
178H TYR* 1.3 76.2 - - - +
180H LEU* 1.3 60.3 + - - +
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Residues in contact with LEU 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143H LEU* 3.9 3.6 - - - +
144H VAL* 2.9 49.9 + - + +
147H TYR* 3.4 23.8 - - + +
150H GLU* 5.5 1.3 - - - +
152H VAL* 3.9 18.4 - - + -
154H VAL* 4.2 2.9 - - + -
167H THR* 4.1 16.8 - - + -
168H PHE* 3.4 24.0 - - - +
169H PRO 4.1 3.1 - - - +
170H ALA* 3.9 15.9 - - + +
179H SER* 1.3 76.2 + - - +
181H SER* 1.3 77.8 + - - +
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Residues in contact with SER 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H LEU* 4.2 17.1 - - - +
142H CYS 3.3 9.9 + - - -
143H LEU* 3.4 23.0 - - - +
167H THR* 3.8 0.3 - - - -
168H PHE* 3.1 46.8 + - - +
180H LEU* 1.3 77.4 - - - +
182H SER* 1.3 61.3 + - - +
183H VAL* 5.6 1.3 - - - -
130L VAL* 4.3 12.2 - - - +
173L SER* 5.0 5.7 + - - -
175L THR* 5.0 3.5 + - - -
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Residues in contact with SER 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H LEU* 4.9 0.2 - - - +
141H GLY* 3.0 3.6 - - - -
142H CYS* 2.7 39.3 + - - -
144H VAL* 5.3 0.4 - - - +
154H VAL* 3.6 32.5 - - - +
156H TRP* 3.0 25.7 + - - -
165H VAL* 4.1 1.7 - - - +
166H HIS 3.4 4.3 + - - -
167H THR* 3.0 21.7 + - - +
180H LEU* 4.3 1.2 - - - +
181H SER* 1.3 74.6 - - - +
183H VAL* 1.3 61.9 + - - +
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Residues in contact with VAL 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H LEU* 5.1 3.8 - - + -
139H ALA* 4.7 0.4 - - + -
140H LEU 3.2 28.7 - - - +
141H GLY* 4.0 2.7 - - - -
156H TRP* 4.8 0.9 - - - -
165H VAL* 3.4 4.6 - - - +
166H HIS* 2.6 60.6 + - + +
168H PHE* 3.8 20.6 - - + -
181H SER* 5.4 2.7 - - - -
182H SER* 1.3 75.7 + - - +
184H VAL* 1.3 60.2 + - - +
185H THR* 6.1 1.1 - - + -
115L PHE* 4.5 9.9 - - + -
132L LEU* 3.6 38.6 - - + -
134L ASN* 5.0 1.6 - - - +
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Residues in contact with VAL 184 (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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138H ALA 3.8 0.7 - - - +
139H ALA* 3.6 1.7 - - - -
140H LEU* 2.8 64.5 + - + +
156H TRP* 4.2 19.5 - - + +
161H LEU* 4.1 20.4 - - + -
163H SER 3.9 7.9 - - - +
164H GLY 3.2 15.5 - - - +
165H VAL* 3.5 24.7 - - + -
183H VAL* 1.3 76.6 - - - +
185H THR* 1.3 72.3 + - - +
186H VAL* 4.0 4.7 + - + -
196H TYR* 5.2 0.4 - - + -
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Residues in contact with THR 185 (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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137H THR* 4.6 15.9 - - - +
138H ALA 3.3 9.4 - - - +
139H ALA* 4.1 15.9 - - + -
163H SER 4.5 2.3 - - - +
164H GLY* 3.0 25.1 + - - +
166H HIS* 5.6 1.1 - - - +
183H VAL* 6.1 1.3 - - + -
184H VAL* 1.3 79.5 - - - +
186H VAL* 1.3 63.3 + - - +
187H PRO* 5.0 0.2 - - - +
113L PHE* 4.4 10.1 - - + -
132L LEU* 5.4 2.0 - - + -
134L ASN* 3.5 33.1 + - - +
135L ASN* 4.9 2.3 + - - -
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Residues in contact with VAL 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H THR* 3.1 9.1 - - - -
138H ALA* 2.6 50.8 + - + +
140H LEU* 4.2 17.9 - - + -
161H LEU* 4.7 6.5 - - + -
184H VAL* 4.3 16.2 - - + +
185H THR* 1.3 80.1 - - - +
187H PRO* 1.4 80.6 - - + +
190H SER* 4.3 0.2 - - - +
191H LEU* 5.2 5.8 - - + -
196H TYR* 3.4 42.0 - - + +
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Residues in contact with PRO 187 (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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136H GLY 3.5 8.7 - - - +
137H THR* 4.3 5.2 - - + -
186H VAL* 1.4 95.0 - - + +
188H SER* 1.3 63.2 + - - +
189H SER* 3.3 11.7 - - - +
190H SER* 2.6 35.5 + - - +
191H LEU* 3.8 1.6 + - - +
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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