Contacts of the helix formed by residues 162 - 167 (chain D) in PDB entry 1T5A
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 LYS 162 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D LEU* 2.9 42.8 - - + +
146D ASN* 3.0 43.1 + - - +
158D TRP* 4.3 11.4 - - - -
159D LEU 4.5 3.6 - - - +
160D ASP 2.8 17.2 + - - +
161D TYR* 1.3 71.7 - - - +
163D ASN* 1.3 57.6 + - - +
164D ILE 2.9 8.3 + - - -
165D CYS* 4.5 0.9 + - - +
166D LYS* 5.5 2.4 - - - -
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Residues in contact with ASN 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D TYR* 3.5 26.0 + - + -
162D LYS* 1.3 77.0 - - - +
164D ILE* 1.3 63.4 + - - +
165D CYS 3.6 1.1 - - - -
166D LYS* 3.2 52.8 + - - +
167D VAL* 3.8 3.1 + - - +
217D ASP* 3.6 23.4 + - - +
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Residues in contact with ILE 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ILE* 6.1 0.4 - - + -
142D ILE* 4.5 1.3 - - + -
144D LEU* 3.5 30.5 - - + -
159D LEU* 3.5 28.3 - - + -
161D TYR* 3.1 42.1 + - + +
162D LYS 2.9 3.6 - - - -
163D ASN* 1.3 76.8 - - - +
165D CYS* 1.3 70.8 + - - +
166D LYS 2.9 2.1 + - - -
167D VAL* 3.0 11.6 + - - +
168D VAL* 3.0 28.5 + - + +
174D ILE* 4.5 10.3 - - + -
193D LEU* 3.8 20.4 - - + -
211D LEU* 4.5 18.2 - - + -
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Residues in contact with CYS 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D LEU* 4.4 9.9 - - + -
162D LYS 4.5 1.0 + - - +
163D ASN 3.6 0.8 - - - -
164D ILE* 1.3 80.9 - - - +
166D LYS* 1.3 64.5 + - + +
167D VAL 3.4 0.4 - - - -
168D VAL* 3.5 15.4 - - - +
188D LYS* 3.2 30.8 + - + +
189D GLY 4.2 4.0 - - - +
190D ALA 4.2 13.5 - - - +
191D ASP* 4.0 7.4 - - - -
192D PHE* 3.4 41.1 - - - -
193D LEU* 3.7 15.7 - - + -
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Residues in contact with LYS 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D LYS 5.5 1.3 - - - -
163D ASN* 3.2 45.2 - - - +
164D ILE 2.9 1.2 + - - -
165D CYS* 1.3 81.9 - - + +
167D VAL* 1.3 61.6 + - + +
168D VAL 4.8 0.7 - - - -
169D GLU* 5.6 1.5 - - - +
188D LYS* 5.6 2.4 + - - +
190D ALA 6.1 0.9 - - - -
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Residues in contact with VAL 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D TYR* 3.3 41.5 - - + +
163D ASN* 4.0 4.7 - - - +
164D ILE 3.0 14.8 + - - +
166D LYS* 1.3 84.1 - - + +
168D VAL* 1.3 62.0 + - - +
169D GLU* 4.1 8.1 + - - +
211D LEU* 4.6 9.2 - - + -
214D ALA* 4.2 15.9 - - + +
215D ALA* 3.5 27.0 + - + +
216D VAL* 4.6 4.3 - - + -
217D ASP* 3.6 13.7 - - - +
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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