Contacts of the strand formed by residues 185 - 194 (chain H) in PDB entry 3INU
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 185 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H ASP* 3.0 9.5 + - - -
147H TYR* 2.8 65.4 + - + +
148H PHE* 3.9 28.9 - + - -
149H PRO* 4.3 0.9 - - + -
150H GLU* 3.7 41.1 - - + +
176H ALA* 3.9 18.6 - - + -
177H VAL 3.6 8.5 - - - -
178H LEU* 3.7 31.0 - - + +
179H GLN* 3.6 0.9 - - - -
184H LEU* 1.3 74.1 - - - +
186H SER* 1.3 59.7 + - - +
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Residues in contact with SER 186 (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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143H LEU* 4.0 10.3 - - - +
144H VAL 3.4 4.6 + - - -
145H LYS* 3.4 24.9 - - - +
147H TYR* 4.0 1.8 - - - -
176H ALA* 3.3 1.9 - - - -
177H VAL* 2.8 41.7 + - - +
179H GLN* 3.3 34.3 + - - -
185H TYR* 1.3 73.1 - - - +
187H LEU* 1.3 61.1 + - - +
178L THR* 6.1 0.7 - - - +
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Residues in contact with LEU 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143H LEU* 3.8 3.3 - - - +
144H VAL* 2.7 49.4 + - + +
147H TYR* 3.5 24.5 - - + +
150H GLU* 5.0 1.8 - - - +
152H VAL* 3.6 26.0 - - + +
154H VAL* 4.1 13.5 - - + -
173H THR* 4.4 9.6 - - + -
174H PHE* 3.5 20.0 - - - +
175H PRO 4.9 2.0 - - - -
176H ALA* 3.9 11.7 - - + +
177H VAL* 5.7 0.2 - - - -
186H SER* 1.3 78.5 + - - +
188H SER* 1.3 75.7 + - - +
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Residues in contact with SER 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU* 4.6 10.8 - - - -
142H CYS 3.3 12.8 - - - -
143H LEU* 4.2 15.3 - - - -
174H PHE* 2.9 41.5 + - - +
187H LEU* 1.3 81.5 - - - +
189H SER* 1.3 61.5 + - - +
190H VAL* 5.3 1.9 - - - +
133L VAL* 5.3 3.3 - - - +
176L SER* 3.0 29.0 + - - -
178L THR* 5.2 2.0 + - - -
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Residues in contact with SER 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141H GLY* 3.0 3.3 - - - -
142H CYS* 2.8 39.9 + - - +
144H VAL* 5.9 0.2 - - - -
154H VAL* 3.5 25.0 - - - +
157H TRP* 2.8 26.5 + - - -
171H VAL* 4.2 1.2 - - - +
172H HIS 3.5 3.7 + - - -
173H THR* 2.9 26.4 + - - +
187H LEU* 4.3 1.0 - - - +
188H SER* 1.3 73.0 - - - +
190H VAL* 1.3 65.2 + - - +
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Residues in contact with VAL 190 (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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124H LEU* 4.5 14.1 - - + -
139H ALA* 5.5 0.2 - - + -
140H LEU 3.3 12.6 - - - +
141H GLY* 4.4 3.4 - - - -
157H TRP* 4.8 1.3 - - - -
169H GLY 5.3 0.4 - - - +
171H VAL* 3.3 4.2 - - - +
172H HIS* 2.6 64.9 + - + +
174H PHE* 3.6 21.1 - - + -
188H SER* 4.3 2.4 - - - +
189H SER* 1.3 81.4 + - - +
191H VAL* 1.3 63.4 + - - +
192H THR* 6.0 1.3 - - + -
118L PHE* 5.1 6.3 - - + -
133L VAL* 6.0 2.5 - - + -
135L LEU* 4.1 32.1 - - + -
137L ASN* 5.2 0.9 - - - +
176L SER* 6.0 0.4 - - - +
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Residues in contact with VAL 191 (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 0.3 - - - +
139H ALA* 3.4 4.3 - - - +
140H LEU* 2.8 66.1 + - + +
157H TRP* 4.2 12.8 - - + -
166H LEU* 3.8 26.0 - - + -
168H SER 3.7 21.3 - - - +
169H GLY 3.5 4.5 - - - -
171H VAL* 4.0 13.7 - - + -
190H VAL* 1.3 76.7 - - - +
192H THR* 1.3 73.3 + - - +
193H VAL* 3.8 11.9 - - + -
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Residues in contact with THR 192 (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* 4.9 13.0 - - - +
138H ALA 3.3 5.6 - - - +
139H ALA* 4.0 20.4 - - + +
168H SER 4.2 7.3 - - - +
169H GLY* 3.4 21.7 + - - +
172H HIS* 6.2 0.2 - - + -
190H VAL* 6.0 2.0 - - + -
191H VAL* 1.3 82.2 - - - +
193H VAL* 1.3 67.4 + - - +
116L PHE* 4.9 4.5 - - + -
135L LEU* 5.3 1.8 - - + -
137L ASN* 3.4 31.2 + - - +
138L ASN* 5.6 0.5 + - - -
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Residues in contact with VAL 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H THR* 3.2 7.5 - - - -
138H ALA* 2.7 41.7 + - + +
140H LEU* 3.9 17.9 - - + -
166H LEU* 4.7 5.2 - - + -
191H VAL* 3.8 23.1 - - + -
192H THR* 1.3 80.7 - - - +
194H PRO* 1.3 78.7 - - + +
198H LEU* 4.1 9.2 - - + -
206H TYR* 3.5 37.7 - - + +
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Residues in contact with PRO 194 (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 3.5 7.6 - - - +
137H THR* 4.4 5.4 - - + -
193H VAL* 1.3 91.4 - - + +
195H SER* 1.3 65.1 + - - +
196H SER* 3.6 19.1 - - - +
197H SER* 2.7 36.3 + - - +
198H LEU* 3.8 1.2 + - - +
206H TYR* 4.7 1.8 - - - +
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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