Contacts of the strand formed by residues 170 - 178 (chain H) in PDB entry 6JOD
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 VAL 170 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H VAL 5.2 2.5 - - - +
161H TRP* 4.3 11.4 - - + -
167H SER* 3.6 36.2 + - - +
168H SER 4.1 1.5 - - - +
169H SER* 1.3 74.3 - - - +
171H HIS* 1.3 68.7 + - - +
172H THR* 3.8 14.3 + - - +
186H SER* 3.7 21.3 - - - +
187H SER 3.3 4.3 - - - +
188H VAL* 3.5 22.9 - - + -
166L ASP* 4.9 7.0 + - - +
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Residues in contact with HIS 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169H SER* 3.6 22.0 + - - -
170H VAL* 1.3 77.0 + - - +
172H THR* 1.3 63.0 + - - +
173H PHE* 3.6 17.9 - - + -
186H SER* 3.3 3.3 - - - -
187H SER* 2.9 57.1 + - - +
189H THR* 5.0 4.0 + - - -
136L ASN* 4.1 10.5 - - - +
137L ASN* 3.0 30.6 + - - -
163L THR* 4.6 7.8 + - + +
166L ASP* 3.8 29.5 + - + +
171L THR* 5.1 0.7 - - - -
172L TYR 5.6 0.4 - - - -
173L SER* 3.1 23.0 + - - -
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Residues in contact with THR 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157H VAL 5.8 2.0 - - - +
159H VAL* 4.8 11.0 + - + +
170H VAL* 3.8 12.1 + - - +
171H HIS* 1.3 71.2 - - - +
173H PHE* 1.3 64.6 + - - +
174H PRO* 3.6 7.6 - - + +
184H MET* 3.8 24.0 - - + -
185H SER 3.9 2.7 - - - -
186H SER* 3.8 12.1 + - - +
163L THR* 3.7 9.1 - - - +
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Residues in contact with PHE 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171H HIS* 3.6 16.2 - - + -
172H THR* 1.3 74.9 - - - +
174H PRO* 1.3 71.8 - - - +
184H MET* 3.5 21.1 - - - +
185H SER* 2.9 43.1 + - - +
187H SER* 3.8 20.4 - - - -
134L PHE* 3.5 33.4 - + - -
136L ASN* 3.9 8.5 - - - -
161L SER* 3.4 32.5 - - - +
163L THR* 3.4 16.6 - - + -
173L SER* 3.8 5.4 - - - -
174L MET* 3.3 15.5 - - - -
175L SER* 3.3 18.4 - - - -
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Residues in contact with PRO 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H GLU* 5.1 8.5 - - - +
172H THR* 3.7 7.2 - - + +
173H PHE* 1.3 88.1 - - - +
175H ALA* 1.3 68.4 + - - +
176H LEU* 3.7 4.5 + - + +
183H THR 4.1 3.1 - - - +
184H MET* 4.3 1.2 - - - +
161L SER* 2.9 26.4 + - - +
162L TRP 3.3 28.9 - - - +
163L THR* 4.2 5.4 - - + -
164L ASP 5.6 0.9 - - - +
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Residues in contact with ALA 175 (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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42H GLU* 4.3 13.2 + - - +
152H TYR* 3.2 26.9 - - - +
155H GLU* 3.4 27.6 + - - +
173H PHE 3.7 0.6 + - - -
174H PRO* 1.3 76.0 - - - +
176H LEU* 1.3 66.9 + - - +
182H TYR* 3.7 12.7 - - + -
183H THR 3.3 11.0 - - - +
184H MET* 4.0 4.7 - - + +
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Residues in contact with LEU 176 (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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42H GLU* 6.0 0.4 - - - +
174H PRO* 4.1 11.9 - - + +
175H ALA* 1.3 84.2 - - - +
177H LEU* 1.3 62.1 + - - +
178H GLN* 3.6 2.9 + - - +
182H TYR* 3.4 4.4 - - - -
183H THR* 2.9 38.1 + - - +
159L LEU* 4.2 36.3 - - + -
160L ASN 3.2 32.1 - - - +
161L SER* 4.1 11.2 - - - +
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Residues in contact with LEU 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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153H PHE* 4.9 5.2 - - + -
176H LEU* 1.3 70.6 - - - +
178H GLN* 1.3 59.2 + - - +
179H SER 4.4 0.2 - - - -
180H GLY* 3.7 14.1 - - - +
181H LEU* 3.5 33.9 - - - +
182H TYR* 3.8 39.6 - - + +
159L LEU* 5.8 0.2 - - - -
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Residues in contact with GLN 178 (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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150H LYS* 4.6 14.5 - - - +
176H LEU 4.4 2.2 - - - +
177H LEU* 1.3 73.1 - - - +
179H SER* 1.3 80.5 + - - +
180H GLY 3.1 1.6 - - - -
181H LEU* 2.9 24.2 + - + +
183H THR* 2.6 40.5 + - - +
159L LEU* 3.3 32.2 - - + +
179L THR* 5.2 12.2 + - - +
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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
------------------------------------------------------------
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