Contacts of the helix formed by residues 168 - 175 (chain D) in PDB entry 4K9N
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 ASP 168 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288C TYR* 4.5 12.0 + - - -
7D THR* 5.3 0.3 + - - +
133D ALA* 4.4 22.6 + - + +
167D ALA* 1.3 73.4 - - - +
169D PRO* 1.3 75.5 - - - +
170D GLN* 2.9 38.2 + - - +
171D SER* 2.9 32.5 + - - +
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Residues in contact with PRO 169 (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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167D ALA 3.4 8.7 - - - +
168D ASP* 1.3 92.0 - - - +
170D GLN* 1.3 60.8 + - + +
171D SER 3.0 4.1 + - - -
172D HIS* 3.0 26.4 + - - +
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Residues in contact with GLN 170 (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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286C GLY 3.6 19.5 - - - +
287C GLN* 3.2 29.6 - - - +
288C TYR* 2.9 37.4 + - + +
289C LEU 5.3 0.2 + - - -
309C PRO 4.9 0.7 - - - +
168D ASP* 2.9 22.2 + - - +
169D PRO* 1.3 78.1 - - + +
171D SER* 1.3 63.8 + - - +
172D HIS* 3.0 19.7 + - - -
173D HIS* 2.8 46.3 + - - +
174D LEU* 4.8 0.3 + - - +
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Residues in contact with SER 171 (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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288C TYR* 5.8 0.7 - - - -
7D THR* 3.8 23.8 - - - -
133D ALA 4.5 4.2 + - - -
136D PRO* 3.9 15.1 - - - +
137D HIS* 5.0 2.3 + - - +
168D ASP* 2.9 30.4 + - - +
170D GLN* 1.3 76.4 - - - +
172D HIS* 1.3 64.2 + - - +
173D HIS 3.1 0.2 - - - -
174D LEU* 3.0 37.3 + - - +
175D PHE* 4.1 7.5 - - - -
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Residues in contact with HIS 172 (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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14D ARG* 5.2 1.0 + - - -
169D PRO 3.0 22.5 + - - +
170D GLN* 3.0 16.7 - - - -
171D SER* 1.3 78.3 - - - +
173D HIS* 1.3 98.9 + + - +
174D LEU 3.0 1.7 + - - -
175D PHE* 3.1 44.8 + - + +
176D ASP 4.7 0.5 + - - -
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Residues in contact with HIS 173 (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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288C TYR* 4.1 8.1 - + + -
289C LEU* 3.7 37.4 + - + +
290C LYS 5.5 1.8 - - - -
291C PRO* 6.4 0.4 - - + -
309C PRO 3.3 20.0 - - - +
310C MET* 3.7 18.8 - - + +
311C GLY 4.5 1.4 + - - -
170D GLN* 2.8 47.0 + - - +
171D SER 3.1 1.0 - - - -
172D HIS* 1.3 105.4 + + - +
174D LEU* 1.3 59.5 + - - +
175D PHE 3.6 0.2 + - - -
176D ASP 4.4 2.9 + - - -
177D ARG* 3.5 15.2 + - - +
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Residues in contact with LEU 174 (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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308C ALA 4.4 2.9 - - - +
309C PRO* 3.4 31.6 - - + +
7D THR* 5.8 0.4 - - + -
11D LEU* 3.6 21.6 - - + +
15D GLN* 3.9 2.6 + - - -
136D PRO* 3.6 34.5 - - + +
137D HIS* 3.6 24.7 - - + +
140D SER* 3.8 20.5 + - - +
144D HIS* 5.2 0.2 + - - -
170D GLN 5.2 0.2 - - - +
171D SER* 3.3 26.2 - - - +
172D HIS 3.0 0.8 - - - -
173D HIS* 1.3 78.1 - - - +
175D PHE* 1.3 66.8 + - + +
176D ASP 3.2 1.5 + - - -
177D ARG* 3.3 20.0 + - - +
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Residues in contact with PHE 175 (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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7D THR* 3.5 39.0 - - + -
10D GLU* 3.6 22.2 - - + -
11D LEU* 3.6 28.0 - - + -
14D ARG* 3.4 58.8 - - + +
15D GLN* 3.0 18.5 + - - +
171D SER 4.1 10.1 - - - -
172D HIS* 3.1 36.6 + - + +
174D LEU* 1.3 78.7 - - + +
176D ASP* 1.3 58.9 + - - +
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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