Contacts of the helix formed by residues 164 - 169 (chain C) in PDB entry 1T9D
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163C SER* 1.3 74.6 - - - +
165C PRO* 1.3 66.2 - - - +
167C ALA* 3.1 6.7 + - - +
168C THR* 3.0 32.0 + - - +
190C GLN* 6.0 0.2 - - - -
202C GLN 3.0 14.9 + - - -
204C ALA* 4.0 16.9 - - - +
206C VAL* 5.1 1.8 - - - +
522D LEU* 3.7 13.7 - - - -
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Residues in contact with PRO 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C SER 3.2 6.3 - - - +
164C GLY* 1.3 80.8 - - - +
166C GLY* 1.3 65.4 + - - +
168C THR* 3.2 10.7 + - - +
169C ASN* 3.0 30.8 + - - -
202C GLN* 3.9 10.8 - - + +
2703C PYD 3.4 35.4 - - + +
172D THR* 4.8 1.1 - - + -
522D LEU* 3.3 35.6 - - + +
523D GLY 3.7 2.7 - - - +
524D THR* 3.9 22.9 - - + +
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Residues in contact with GLY 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C GLU* 3.5 37.5 - - - +
161C VAL* 3.5 13.3 - - - +
162C THR* 3.7 18.1 - - - +
163C SER 3.0 11.2 + - - -
165C PRO* 1.3 81.7 - - - +
167C ALA* 1.3 61.4 + - - +
169C ASN 3.6 4.2 + - - -
170C VAL* 3.7 2.6 - - - +
2703C PYD 4.4 0.6 - - - -
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Residues in contact with ALA 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C VAL* 4.2 2.9 - - - -
162C THR 3.3 11.7 + - - +
163C SER* 4.5 0.4 - - - -
164C GLY 3.1 9.7 + - - +
166C GLY* 1.3 73.2 - - - +
168C THR* 1.3 62.8 + - - +
169C ASN 3.1 1.8 - - - -
170C VAL* 2.9 29.1 + - - +
171C VAL* 3.8 7.0 + - - +
174C MET* 4.7 2.1 - - - +
188C THR* 3.9 17.9 - - + -
206C VAL* 3.4 36.4 - - + +
246C LEU* 5.7 0.2 - - + -
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Residues in contact with THR 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C GLY 3.0 15.8 + - - +
165C PRO* 3.2 18.0 + - - +
167C ALA* 1.3 77.4 - - + +
169C ASN* 1.3 61.7 + - - +
170C VAL 3.1 1.3 + - - -
171C VAL* 3.3 24.9 + - + +
204C ALA* 4.4 7.0 - - + -
206C VAL* 5.8 0.9 - - + -
209C ILE* 4.3 21.8 - - + -
168D THR 5.0 2.1 - - - +
171D VAL* 4.2 12.2 - - + +
172D THR* 2.7 34.8 + - - +
175D ALA* 4.2 21.5 - - + -
522D LEU* 4.7 1.1 - - + +
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Residues in contact with ASN 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C HIS* 3.3 27.9 + - + -
139C GLU* 3.0 34.8 - - + +
140C GLN* 3.4 25.6 - - - +
165C PRO 3.0 18.2 + - - +
166C GLY 3.7 0.4 - - - +
167C ALA 3.1 0.6 - - - -
168C THR* 1.3 76.9 + - - +
170C VAL* 1.3 58.1 + - - +
171C VAL 3.5 0.4 - - - -
172C THR* 4.9 1.1 + - - -
173C PRO* 4.1 2.6 - - - +
2703C PYD 3.3 18.1 - - - +
140D GLN* 4.1 8.2 + - - +
172D THR* 2.6 40.0 + - - +
525D MET 5.3 0.2 - - - +
555D MET* 4.4 0.2 - - - +
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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
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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