Contacts of the strand formed by residues 176 - 185 (chain H) in PDB entry 3P11
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 176 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144H ASP* 2.8 27.4 + - - -
145H TYR* 3.3 41.1 + - + +
146H PHE* 4.5 18.2 - + - -
148H GLU* 3.9 34.1 - - + +
168H ALA* 3.6 17.7 - - + -
169H VAL* 3.5 16.6 - - - -
170H LEU* 3.5 40.9 - - + +
171H GLN* 4.3 0.2 + - - -
175H LEU* 1.3 74.8 - - - +
177H SER* 1.3 60.5 + - - +
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Residues in contact with SER 177 (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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141H LEU* 3.7 9.9 - - - +
142H VAL 3.2 13.7 + - - -
143H LYS* 3.6 14.7 - - - +
145H TYR* 3.8 3.6 - - - -
167H PRO 4.1 0.5 - - - +
168H ALA* 3.2 3.9 - - - -
169H VAL* 2.9 33.8 + - - +
171H GLN* 3.2 25.8 - - - -
176H TYR* 1.3 78.6 - - - +
178H LEU* 1.3 64.3 + - - +
160L GLN* 5.6 3.1 - - - -
178L THR* 5.6 3.6 + - - +
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Residues in contact with LEU 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141H LEU* 3.4 7.6 - - - +
142H VAL* 2.9 49.7 + - + +
145H TYR* 3.5 20.2 - - - +
148H GLU* 5.3 2.0 - - - +
150H VAL* 4.3 18.8 - - + +
152H VAL* 4.6 1.6 - - + -
165H THR* 3.6 23.1 - - + -
166H PHE 3.4 20.6 - - - +
167H PRO 3.6 9.0 - - - +
168H ALA* 3.8 7.6 - - + +
177H SER* 1.3 79.6 + - - +
179H SER* 1.3 75.6 - - - +
180H SER* 4.1 2.5 - - - +
162L SER* 6.2 1.3 - - - -
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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
----------------------------------------------------------
124H LEU* 4.0 12.5 - - - +
140H CYS 3.6 7.4 - - - -
141H LEU* 4.1 9.5 - - - +
166H PHE* 3.0 47.3 + - - +
178H LEU* 1.3 80.0 - - - +
180H SER* 1.3 62.2 + - - +
181H VAL* 5.5 2.2 - - - -
133L VAL* 3.9 22.4 - - - +
176L SER* 4.0 14.5 + - - -
178L THR* 5.0 3.3 + - - -
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Residues in contact with SER 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU* 5.9 0.4 - - - -
139H GLY* 3.2 2.3 - - - -
140H CYS* 2.7 44.2 + - - +
142H VAL* 5.5 1.1 - - - +
152H VAL* 3.5 23.6 - - - +
154H TRP* 3.5 19.3 + - - -
163H VAL* 4.4 0.2 - - - +
164H HIS 3.2 6.7 + - - -
165H THR* 2.8 30.5 + - - -
178H LEU* 4.1 3.1 - - - +
179H SER* 1.3 74.8 - - - +
181H VAL* 1.3 60.3 + - - +
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Residues in contact with VAL 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU* 5.8 2.9 - - + -
137H ALA* 4.8 4.9 - - + -
138H LEU 3.4 20.2 - - - +
139H GLY* 4.3 2.5 - - - -
154H TRP* 4.8 2.0 - - - -
163H VAL* 3.6 1.6 - - - +
164H HIS* 2.5 67.6 + - + +
166H PHE* 4.0 16.8 - - + -
179H SER* 5.5 3.1 - - - -
180H SER* 1.3 74.9 - - - +
182H VAL* 1.3 61.5 + - - +
183H THR* 5.9 2.0 - - + -
118L PHE* 4.0 25.1 - - + -
135L LEU* 4.3 22.2 - - + -
137L ASN* 4.8 0.9 - - - +
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Residues in contact with VAL 182 (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 ALA* 3.7 1.0 - - - +
138H LEU* 3.0 52.8 + - + +
154H TRP* 4.1 16.2 - - + +
159H LEU* 3.9 23.8 - - + -
161H SER 3.7 11.7 - - - +
162H GLY 3.4 15.0 - - - +
163H VAL* 3.7 24.0 - - + -
181H VAL* 1.3 78.3 - - - +
183H THR* 1.3 75.0 + - - +
184H VAL* 4.1 5.6 + - + -
194H TYR* 5.5 0.7 - - + -
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Residues in contact with THR 183 (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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135H THR* 4.0 16.2 - - + +
136H ALA 3.5 4.3 - - - +
137H ALA* 4.1 18.8 - - + -
159H LEU* 5.9 0.2 - - - +
161H SER 4.6 4.3 - - - +
162H GLY* 3.5 15.8 + - - +
164H HIS* 6.0 0.2 - - + -
181H VAL* 5.9 2.7 - - + -
182H VAL* 1.3 81.5 - - - +
184H VAL* 1.3 68.1 + - - +
185H PRO* 4.9 0.3 - - - +
116L PHE* 5.0 7.2 - - + -
135L LEU* 5.7 1.1 - - + -
137L ASN* 3.5 28.8 + - - +
138L ASN* 5.8 0.5 + - - -
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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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135H THR* 4.1 3.1 - - - -
136H ALA* 2.8 38.5 + - - +
138H LEU* 4.2 14.4 - - + -
159H LEU* 4.3 7.0 - - + -
182H VAL* 4.3 17.3 - - + -
183H THR* 1.3 80.6 - - - +
185H PRO* 1.3 69.4 - - + +
188H SER* 3.8 5.2 - - - +
189H LEU* 4.4 10.1 - - + -
194H TYR* 3.3 52.5 - - + +
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Residues in contact with PRO 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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134H GLY 4.2 8.3 - - - +
135H THR* 4.4 5.2 - - - +
183H THR 4.9 0.2 - - - +
184H VAL* 1.3 87.6 - - + +
186H SER* 1.3 67.2 + - - +
187H SER* 4.1 13.5 - - - +
188H SER* 2.4 41.3 + - - +
189H LEU* 3.7 1.4 + - - +
194H TYR* 4.9 0.4 - - - +
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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