Contacts of the helix formed by residues 164 - 169 (chain A) in PDB entry 1JSC
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 GLY 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A SER* 1.3 73.2 - - - +
165A PRO* 1.3 63.9 - - - +
167A ALA* 3.1 9.7 + - - +
168A THR* 2.9 31.8 + - - +
202A GLN 3.1 15.5 + - - -
204A ALA* 4.2 14.9 - - - +
206A VAL* 5.3 1.0 - - - +
522B LEU* 3.7 14.4 - - - -
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Residues in contact with PRO 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A SER 3.1 6.7 - - - +
164A GLY* 1.3 83.3 - - - +
166A GLY* 1.3 58.2 + - - +
168A THR* 3.3 11.2 + - - +
169A ASN* 2.9 35.7 + - - -
202A GLN* 3.7 9.2 - - - +
172B THR* 4.8 1.8 - - + +
522B LEU* 3.4 34.6 - - + +
523B GLY 3.7 3.8 - - - +
524B THR* 3.9 25.4 - - + +
1700B TPP 3.4 35.7 - - + +
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Residues in contact with GLY 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A GLU* 3.7 26.9 - - - +
161A VAL* 3.5 13.7 - - - +
162A THR* 3.5 21.9 - - - +
163A SER 3.1 7.0 + - - -
165A PRO* 1.3 82.9 - - - +
167A ALA* 1.3 62.7 + - - +
169A ASN 3.6 4.0 + - - -
170A VAL* 3.7 11.3 - - - +
1700B TPP 4.2 0.4 - - - +
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Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A VAL* 4.1 7.4 - - - -
162A THR 3.2 11.5 + - - +
163A SER* 4.6 0.9 - - - -
164A GLY 3.1 10.4 + - - +
166A GLY* 1.3 74.9 - - - +
168A THR* 1.3 64.9 + - + +
170A VAL* 3.0 21.4 + - - +
171A VAL* 3.8 7.4 + - - +
174A MET* 4.7 1.7 - - - +
188A THR* 3.8 20.0 - - + -
206A VAL* 3.6 36.1 - - + +
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Residues in contact with THR 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLY 2.9 17.7 + - - +
165A PRO* 3.3 15.8 - - - +
167A ALA* 1.3 76.5 - - + +
169A ASN* 1.3 60.9 + - - +
170A VAL 3.1 1.7 + - - -
171A VAL* 3.3 24.2 + - - +
172A THR 5.0 0.2 + - - -
204A ALA* 4.8 7.0 - - + -
206A VAL* 6.0 0.2 - - + -
209A ILE* 4.1 25.6 - - + -
168B THR 5.1 1.7 - - - +
171B VAL* 4.2 12.5 - - + +
172B THR* 2.6 36.5 + - - +
175B ALA* 4.2 19.1 - - + -
522B LEU* 4.7 1.0 - - - +
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Residues in contact with ASN 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A HIS* 3.3 29.4 + - + -
139A GLU* 3.2 30.2 - - + +
140A GLN* 3.4 25.6 - - - +
165A PRO 2.9 20.8 + - - +
166A GLY 4.0 0.2 - - - +
167A ALA 3.2 0.4 - - - -
168A THR* 1.3 76.4 - - - +
170A VAL* 1.3 59.9 + - - +
171A VAL 3.4 1.1 + - - -
172A THR* 4.9 1.1 + - - -
173A PRO* 4.0 2.9 - - - +
140B GLN* 4.2 7.1 + - - +
172B THR* 2.4 41.5 + - - +
524B THR* 5.2 0.5 - - - +
555B MET* 3.4 12.6 - - - +
1700B TPP 3.5 4.0 - - - +
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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