Contacts of the strand formed by residues 185 - 194 (chain H) in PDB entry 1J5O
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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120H THR* 4.1 19.8 - - - +
154H GLY 3.4 5.7 + - - -
155H TYR* 2.7 72.0 + + + +
156H PHE* 2.9 30.3 - + - -
158H GLU* 3.1 43.2 + - + +
178H ALA* 3.9 7.9 - - + -
179H VAL 3.8 3.6 - - - -
180H LEU* 3.2 39.6 - - + +
184H LEU* 1.3 79.4 - - - +
186H THR* 1.3 61.0 + - - +
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Residues in contact with THR 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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151H LEU* 3.9 13.5 - - + -
152H VAL 3.2 3.8 - - - +
153H LYS* 3.6 32.3 - - + +
154H GLY 3.8 2.9 + - - -
178H ALA* 3.1 17.5 - - - +
179H VAL* 3.5 12.3 + - - +
181H GLN* 3.3 36.7 + - - +
184H LEU* 5.7 0.5 - - - +
185H TYR* 1.3 72.8 + - - +
187H LEU* 1.3 62.8 + - - +
160L LEU* 5.4 3.4 - - + -
178L THR* 5.7 9.2 - - + +
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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
----------------------------------------------------------
151H LEU* 3.5 3.7 - - - +
152H VAL* 2.4 68.5 + - + +
155H TYR* 4.2 13.0 - - + +
158H GLU* 5.4 1.8 - - - +
160H VAL* 4.3 16.6 - - + +
162H VAL* 4.9 7.9 - - + -
175H THR* 4.4 16.6 - - + -
176H PHE 3.1 26.5 - - - +
177H PRO* 4.6 1.3 - - + -
178H ALA* 3.6 21.1 - - + +
185H TYR 4.2 0.2 - - - -
186H THR* 1.3 75.8 - - - +
188H SER* 1.3 87.6 + - - +
189H SER* 4.2 2.9 - - - +
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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
----------------------------------------------------------
134H LEU* 4.6 2.5 - - - -
150H CYS 2.9 16.8 - - - -
151H LEU* 4.3 10.8 - - - -
176H PHE* 2.9 29.8 + - - +
187H LEU* 1.3 87.2 - - - +
189H SER* 1.3 63.2 + - - +
133L VAL* 4.4 9.9 - - - +
135L PHE* 3.8 22.8 - - - -
176L SER* 4.7 3.8 + - - -
178L THR* 4.9 5.7 + - - -
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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
----------------------------------------------------------
149H GLY* 3.1 2.1 - - - -
150H CYS* 2.9 31.3 + - - +
152H VAL* 5.6 0.2 - - - +
162H VAL* 5.5 7.9 - - - -
164H TRP* 3.5 13.2 + - - -
173H VAL* 3.9 6.9 - - - +
174H HIS 2.2 28.4 + - - -
175H THR* 2.9 31.9 + - - +
176H PHE* 3.8 3.6 - - - -
187H LEU* 4.2 3.3 - - - +
188H SER* 1.3 76.9 - - - +
190H SER* 1.3 60.7 + - - +
135L PHE* 4.1 2.2 - - - -
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Residues in contact with SER 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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147H THR* 3.9 8.0 - - - +
148H LEU 2.9 15.9 - - - -
149H GLY* 3.8 0.4 - - - -
172H GLY 4.2 0.2 - - - +
173H VAL* 3.3 3.7 - - - +
174H HIS* 2.7 41.6 + - - +
176H PHE* 4.0 8.0 - - - -
189H SER* 1.3 72.3 - - - +
191H VAL* 1.3 61.4 + - - +
135L PHE* 3.3 48.4 - - - +
137L ASN* 4.3 4.3 + - - -
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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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146H VAL 3.6 0.2 - - - +
147H THR* 2.9 4.4 - - - +
148H LEU* 2.4 73.8 + - + +
164H TRP* 3.2 57.0 - - + +
169H LEU* 4.8 3.1 - - + -
172H GLY 3.4 5.8 - - - +
173H VAL* 3.7 17.9 - - + -
190H SER* 1.3 76.0 - - - +
192H THR* 1.3 63.4 + - - +
193H VAL* 4.8 8.7 - - + -
203H VAL* 4.7 5.4 - - + -
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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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145H MET* 4.3 15.5 - - + +
146H VAL* 2.8 31.9 - - - +
147H THR* 2.6 26.0 + - - +
172H GLY* 3.1 23.7 + - - +
191H VAL* 1.3 75.7 + - - +
193H VAL* 1.3 67.3 + - - +
194H PRO* 4.5 1.4 - - - +
137L ASN* 5.8 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
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145H MET* 4.4 2.9 - - - -
146H VAL* 2.7 33.5 + - + +
148H LEU* 4.2 9.4 - - + -
169H LEU* 3.6 31.0 - - + -
191H VAL* 4.8 7.0 - - + -
192H THR* 1.3 84.5 - - - +
194H PRO* 1.3 69.5 - - + +
195H SER 3.5 0.2 + - - -
197H THR* 3.2 20.2 - - - +
198H TRP* 3.6 28.9 - - + +
203H VAL* 4.8 5.8 - - + -
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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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144H SER 4.1 1.3 - - - +
145H MET* 3.4 31.4 - - + -
192H THR 4.5 1.6 - - - +
193H VAL* 1.3 89.5 - - + +
195H SER* 1.3 68.3 + - - +
196H SER* 3.4 7.6 - - - +
197H THR* 2.4 46.0 + - + +
198H TRP 3.5 1.4 + - - -
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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