Contacts of the helix formed by residues 154 - 168 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A ASP 4.3 0.6 + - - -
150A PHE* 2.9 40.3 + - + +
153A ASN* 1.3 69.5 - - - +
155A HIS* 1.3 58.7 + - - +
156A PRO* 3.6 13.4 - - - +
157A ASN* 3.1 35.2 + - - +
158A ARG* 2.9 27.9 + - - +
178A ARG* 5.2 1.7 + - - -
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Residues in contact with HIS 155 (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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152A ASP 3.5 18.1 + - - -
153A ASN* 3.0 26.3 + - + -
154A ASP* 1.3 71.1 - - - +
156A PRO* 1.3 72.4 - - + +
158A ARG* 3.3 30.6 - - - +
159A VAL* 2.9 30.0 + - - +
255A LEU* 3.4 37.3 - - + +
256A PRO* 5.9 0.9 - - + -
259A TRP* 3.9 33.6 - + + -
435A THR* 4.1 6.7 - - + -
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Residues in contact with PRO 156 (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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153A ASN 5.0 1.1 - - - +
154A ASP* 3.6 13.2 - - - +
155A HIS* 1.3 94.9 - - + +
157A ASN* 1.3 63.2 + - - +
159A VAL* 3.7 4.3 - - - +
160A LEU* 3.1 22.9 + - - +
259A TRP* 3.8 33.6 - - + +
261A SER* 4.6 4.2 + - - -
330A SER* 5.4 2.4 + - - -
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Residues in contact with ASN 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A PHE* 3.9 11.4 - - + -
154A ASP* 3.1 34.9 + - - +
155A HIS 3.2 0.4 - - - -
156A PRO* 1.3 82.2 - - - +
158A ARG* 1.3 57.0 + - - +
159A VAL 3.1 1.8 - - - -
160A LEU* 3.4 22.2 - - - +
161A GLU* 2.8 34.3 + - - +
178A ARG* 5.2 7.0 + - - +
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Residues in contact with ARG 158 (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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150A PHE* 3.6 19.9 - - + +
151A GLU* 3.1 60.6 + - - +
154A ASP 2.9 19.3 + - - +
155A HIS* 3.3 37.1 - - - +
157A ASN* 1.3 76.6 - - - +
159A VAL* 1.3 59.9 + - + +
161A GLU* 3.4 3.0 + - - +
162A HIS* 2.8 41.1 + - - +
250A LEU* 4.4 21.1 + - + +
252A ASP* 5.9 2.2 - - - +
255A LEU* 5.1 1.0 - - - +
435A THR* 3.5 31.1 + - - +
34E TYR* 3.8 0.6 + - - -
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Residues in contact with VAL 159 (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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155A HIS 2.9 20.3 + - - +
156A PRO* 3.7 5.4 - - + +
158A ARG* 1.3 77.8 - - + +
160A LEU* 1.3 63.4 + - - +
162A HIS* 3.1 8.3 + - - +
163A LEU* 2.9 22.3 + - - +
250A LEU* 5.6 2.7 - - + -
259A TRP* 3.9 13.0 - - + +
260A ILE 4.3 0.7 - - - -
261A SER* 3.6 23.8 - - - +
433A ALA* 3.7 28.3 - - + +
434A GLY 4.3 1.6 - - - -
435A THR* 3.2 36.6 - - + +
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Residues in contact with LEU 160 (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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156A PRO 3.1 12.5 + - - +
157A ASN* 3.1 27.7 + - - +
159A VAL* 1.3 80.6 - - - +
161A GLU* 1.3 57.1 + - - +
163A LEU* 3.4 19.8 - - + +
164A HIS* 2.9 34.0 + - + -
261A SER* 4.4 5.6 - - - +
317A PHE* 4.2 23.1 - - + -
319A LEU* 4.6 9.2 - - + -
330A SER* 4.0 22.7 - - - +
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Residues in contact with GLU 161 (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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98A ARG* 3.0 34.8 + - - +
150A PHE* 4.5 5.5 - - + -
157A ASN 2.8 16.1 + - - +
158A ARG* 3.7 6.3 - - - +
159A VAL 3.2 0.2 - - - -
160A LEU* 1.3 75.8 - - - +
162A HIS* 1.3 59.9 + - - +
164A HIS* 3.4 10.5 + - - +
165A SER* 3.1 22.3 + - - -
176A PRO* 3.6 22.0 - - + +
177A THR* 3.2 31.4 + - - +
178A ARG* 3.4 23.9 + - - +
34E TYR* 3.9 13.3 - - + +
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Residues in contact with HIS 162 (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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151A GLU* 3.1 26.9 - - - -
158A ARG* 2.8 32.5 + - + +
159A VAL* 3.1 8.7 + - - +
161A GLU* 1.3 74.0 - - - +
163A LEU* 1.3 65.0 + - - +
164A HIS 3.2 0.2 - - - -
165A SER* 3.3 8.6 - - - -
166A THR* 3.0 23.6 + - - +
248A VAL* 3.8 19.9 - - + +
250A LEU* 3.5 28.4 - - + +
433A ALA* 4.4 4.0 - - + -
33E THR* 2.8 42.2 + - - -
34E TYR* 3.3 20.0 + + - -
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Residues in contact with LEU 163 (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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159A VAL 2.9 11.0 + - - +
160A LEU* 3.4 17.9 - - + +
161A GLU 3.2 0.4 - - - -
162A HIS* 1.3 78.3 - - - +
164A HIS* 1.3 51.8 + - - +
166A THR* 3.2 5.1 - - + +
167A ALA* 2.7 40.9 + - + +
261A SER* 4.1 23.1 - - - +
263A ALA* 4.0 21.8 - - + +
317A PHE* 4.3 15.9 - - + -
326A LEU* 4.0 20.0 - - + -
431A ALA* 3.5 40.8 - - + +
432A ILE 4.3 1.8 - - - +
433A ALA* 3.9 8.7 - - + +
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Residues in contact with HIS 164 (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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98A ARG* 3.5 31.8 + - - +
160A LEU* 2.9 34.4 + - + -
161A GLU* 3.4 8.3 + - - +
163A LEU* 1.3 74.6 - - - +
165A SER* 1.3 68.3 + - - +
167A ALA* 4.3 0.9 - - - -
168A PHE* 3.0 41.5 + + - +
173A LEU 3.8 7.6 - - - +
174A SER* 3.5 4.0 - - - -
319A LEU* 4.0 15.3 - - + +
321A TYR* 2.9 41.7 + + - -
326A LEU* 3.4 27.7 - - + +
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Residues in contact with SER 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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161A GLU 3.1 5.7 + - - -
162A HIS* 3.3 24.2 - - - -
164A HIS* 1.3 80.6 - - - +
166A THR* 1.3 57.1 + - - +
169A GLN* 3.2 27.0 + - - +
174A SER* 3.5 17.4 + - - -
248A VAL* 6.0 0.2 - - - -
33E THR 4.2 1.9 + - - -
34E TYR* 3.1 47.8 + - - +
36E THR* 3.6 7.0 + - - -
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Residues in contact with THR 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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162A HIS 3.0 14.6 + - - +
163A LEU* 3.2 15.9 - - + +
165A SER* 1.3 76.0 - - - +
167A ALA* 1.3 71.6 + - - +
168A PHE 3.2 1.6 - - - -
169A GLN* 3.3 23.2 + - - +
246A SER* 2.9 41.8 + - - +
247A GLU* 3.6 11.1 + - - -
248A VAL* 3.9 24.5 - - + +
431A ALA* 4.6 0.2 - - + -
432A ILE 3.9 12.8 - - - +
36E THR* 4.5 4.6 - - - +
27H TYR* 5.6 3.1 - - - -
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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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163A LEU* 2.7 24.8 + - + +
166A THR* 1.3 75.7 - - - +
168A PHE* 1.3 65.2 + - + +
169A GLN 3.8 0.2 + - - -
242A ALA 3.6 0.2 - - - +
243A PHE* 3.5 25.5 - - + -
244A LEU* 2.8 34.8 + - - +
326A LEU* 3.8 16.6 - - + -
431A ALA* 3.8 17.0 - - + -
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Residues in contact with PHE 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 HIS* 3.0 31.2 + + - +
167A ALA* 1.3 77.7 - - + +
169A GLN* 1.3 67.5 + - - +
171A THR* 3.0 18.3 - - + -
173A LEU* 3.6 29.6 - - + -
174A SER* 3.0 23.2 - - - +
242A ALA 3.1 33.0 - - - +
243A PHE* 4.2 10.5 - + + -
244A LEU* 6.2 0.2 - - - -
321A TYR* 4.7 2.2 - + - -
324A SER* 3.3 30.1 - - - -
325A GLY* 3.5 26.2 - - - -
326A LEU* 3.6 29.4 - - + -
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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