Contacts of the helix formed by residues 154 - 168 (chain L) in PDB entry 1KYO
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 154 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149L ASP 4.2 0.4 + - - -
150L PHE* 3.1 35.6 + - + +
153L ASN* 1.3 72.6 - - - +
155L HIS* 1.3 56.9 + - - +
156L PRO* 3.3 14.2 - - - +
157L ASN* 2.8 41.8 + - - +
158L ARG* 2.9 29.3 + - - +
178L ARG* 5.4 0.3 + - - -
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Residues in contact with HIS 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152L ASP 3.5 18.1 + - - -
153L ASN* 2.9 29.5 + - - -
154L ASP* 1.3 70.8 - - - +
156L PRO* 1.3 72.6 - - + +
158L ARG* 3.0 36.1 + - - +
159L VAL* 2.8 29.6 + - - +
255L LEU* 3.3 40.8 - - + +
256L PRO* 6.0 0.2 - - + -
259L TRP* 3.9 34.5 - + + -
435L THR* 4.0 7.4 - - + -
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Residues in contact with PRO 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153L ASN 4.9 0.2 - - - +
154L ASP* 3.3 18.4 - - - +
155L HIS* 1.3 95.5 - - + +
157L ASN* 1.3 64.4 + - - +
159L VAL* 3.4 6.3 + - + +
160L LEU* 3.2 20.1 + - - +
259L TRP* 4.0 26.7 - - + +
261L SER* 4.6 3.8 + - - -
330L SER* 5.9 2.1 - - - -
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Residues in contact with ASN 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150L PHE* 3.9 13.3 - - + -
154L ASP* 2.8 38.3 + - - +
155L HIS 3.3 0.2 - - - -
156L PRO* 1.3 84.7 - - - +
158L ARG* 1.3 60.0 + - - +
160L LEU* 3.4 16.0 + - - +
161L GLU* 3.0 28.8 + - - +
178L ARG* 5.0 7.3 + - - +
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Residues in contact with ARG 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150L PHE* 3.8 17.4 - - + +
151L GLU* 3.3 60.6 + - - +
152L ASP 4.9 0.2 + - - -
154L ASP 2.9 18.1 + - - +
155L HIS* 3.0 38.1 + - - +
157L ASN* 1.3 76.0 - - - +
159L VAL* 1.3 61.7 + - + +
161L GLU* 3.2 3.2 + - - +
162L HIS* 2.9 40.2 + - + +
250L LEU* 4.1 20.4 + - + +
252L ASP* 5.6 3.4 + - - +
255L LEU* 4.9 2.8 - - - +
435L THR* 3.0 27.1 + - - +
34P TYR* 4.2 0.2 - - - +
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Residues in contact with VAL 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155L HIS 2.8 19.7 + - - +
156L PRO* 3.7 5.8 - - + +
158L ARG* 1.3 77.4 - - + +
160L LEU* 1.3 56.3 + - - +
162L HIS* 3.2 5.5 + - - -
163L LEU* 2.9 22.9 + - - +
250L LEU* 5.0 4.0 - - + -
259L TRP* 4.0 7.9 - - + +
260L ILE* 4.2 4.3 - - - -
261L SER* 3.6 22.2 - - - +
433L ALA* 3.4 36.0 - - - +
434L GLY 4.2 1.8 - - - -
435L THR* 3.3 39.7 - - + +
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Residues in contact with LEU 160 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156L PRO 3.2 15.0 + - - +
157L ASN* 3.6 18.8 - - - +
158L ARG 3.2 0.4 - - - -
159L VAL* 1.3 75.7 - - - +
161L GLU* 1.3 63.8 + - - +
163L LEU* 3.0 25.0 + - + +
164L HIS* 3.1 25.2 + - + -
261L SER* 4.2 10.3 + - - +
317L PHE* 4.2 22.9 - - + -
319L LEU* 4.7 17.5 - - + -
326L LEU* 5.9 0.2 - - + -
330L SER* 4.0 20.9 - - - +
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Residues in contact with GLU 161 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98L ARG* 3.0 34.8 + - - -
150L PHE* 4.7 4.0 - - + -
157L ASN 3.0 16.7 + - - +
158L ARG* 3.2 7.4 + - - +
160L LEU* 1.3 75.6 - - - +
162L HIS* 1.3 58.5 + - - +
164L HIS* 3.2 7.5 + - - +
165L SER* 3.0 24.8 + - - -
176L PRO* 3.7 26.9 - - + +
177L THR* 3.4 10.0 + - - -
178L ARG* 3.0 34.9 + - - -
34P TYR* 3.5 21.7 - - + +
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Residues in contact with HIS 162 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151L GLU* 3.1 28.5 - - - -
158L ARG* 2.9 27.0 + - + +
159L VAL 3.6 5.4 - - - +
160L LEU 3.2 0.2 - - - -
161L GLU* 1.3 73.6 - - - +
163L LEU* 1.3 61.0 + - - +
165L SER* 3.3 8.4 - - - -
166L THR* 2.9 30.7 + - - +
248L VAL* 3.7 18.3 - - + +
250L LEU* 3.7 34.1 - - + +
433L ALA* 4.2 3.6 - - + -
33P THR* 2.8 40.5 + - - -
34P TYR* 3.4 25.9 - + - -
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Residues in contact with LEU 163 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159L VAL 2.9 12.8 + - - +
160L LEU* 3.0 25.1 + - + +
162L HIS* 1.3 78.4 - - - +
164L HIS* 1.3 55.9 + - - +
166L THR* 3.4 3.0 - - + +
167L ALA* 2.8 33.1 + - - +
261L SER* 3.8 19.3 - - - +
262L LEU 4.6 0.2 - - - +
263L ALA* 3.9 20.4 - - + -
317L PHE* 5.1 1.8 - - + -
326L LEU* 3.4 31.0 - - + -
431L ALA* 3.5 36.8 - - + +
432L ILE 3.8 1.3 - - - +
433L ALA* 3.7 22.9 - - + +
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Residues in contact with HIS 164 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98L ARG* 3.3 46.6 + - - +
160L LEU* 3.1 32.4 + - + -
161L GLU* 3.4 3.5 - - - +
162L HIS 3.2 0.2 - - - -
163L LEU* 1.3 75.0 - - - +
165L SER* 1.3 65.4 + - - +
167L ALA* 4.4 1.1 - - - -
168L PHE* 3.0 39.8 + + - +
173L LEU 4.3 3.1 - - - +
174L SER* 3.8 3.5 - - - -
319L LEU* 3.5 22.2 - - + +
321L TYR* 2.7 40.3 + + - -
326L LEU* 3.7 20.1 - - + +
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Residues in contact with SER 165 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161L GLU 3.0 14.5 + - - -
162L HIS* 3.3 17.6 - - - -
164L HIS* 1.3 77.2 - - - +
166L THR* 1.3 55.7 + - - +
169L GLN* 3.2 25.6 - - - +
174L SER* 3.6 20.0 + - - -
176L PRO* 5.7 0.2 - - - -
248L VAL* 6.0 0.2 - - - +
33P THR 4.4 3.3 + - - -
34P TYR* 3.3 41.2 + - - +
36P THR* 3.7 7.2 + - - -
27S TYR* 5.9 0.7 - - - -
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Residues in contact with THR 166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162L HIS 2.9 15.0 + - - +
163L LEU* 3.4 12.1 - - - +
165L SER* 1.3 75.1 - - - +
167L ALA* 1.3 69.5 + - - +
168L PHE 3.2 2.4 + - - -
169L GLN* 3.3 23.2 + - - +
244L LEU 4.0 0.7 - - - +
246L SER* 2.7 50.8 + - - +
247L GLU 3.6 8.7 + - - -
248L VAL* 3.6 24.7 - - + -
431L ALA* 4.5 4.0 - - + -
432L ILE 3.9 12.8 - - - +
36P THR* 5.0 3.4 - - - +
27S TYR* 5.5 3.3 - - - +
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Residues in contact with ALA 167 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163L LEU 2.8 21.4 + - - +
164L HIS* 4.1 2.0 - - - +
166L THR* 1.3 79.5 - - - +
168L PHE* 1.3 61.5 + - + +
243L PHE* 3.3 21.3 - - + -
244L LEU* 3.0 31.5 + - - -
326L LEU* 3.9 16.6 - - + -
431L ALA* 3.5 25.6 - - + -
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Residues in contact with PHE 168 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164L HIS* 3.0 31.8 + + - +
167L ALA* 1.3 80.2 - - + +
169L GLN* 1.3 69.9 + - - +
171L THR* 3.0 19.5 - - + -
173L LEU* 3.5 31.0 - - + -
174L SER* 3.1 21.3 - - - +
242L ALA 3.4 22.4 - - - -
243L PHE* 4.0 18.4 - + + -
244L LEU* 5.9 0.4 - - - -
321L TYR* 4.9 1.8 - + - -
324L SER* 3.7 22.0 - - - -
325L GLY* 3.4 33.4 - - - -
326L LEU* 3.8 23.1 - - + -
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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
------------------------------------------------------------
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