Contacts of the helix formed by residues 160 - 175 (chain A) in PDB entry 5KAL
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 PRO 160 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ASN* 3.4 14.6 - - - +
159A PRO* 1.3 101.0 - - + +
161A CYS* 1.3 61.4 + - - +
162A ARG* 2.9 2.2 + - - +
163A TRP* 2.9 35.8 + - + +
164A LEU 4.3 0.2 + - - -
227A LEU* 5.8 1.3 - - + -
228A GLU 6.1 0.4 - - - +
240A GLN* 5.4 2.4 - - - +
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Residues in contact with CYS 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A PHE* 4.3 10.4 - - + -
158A ASN* 3.2 40.9 + - + +
159A PRO 3.0 1.0 + - - -
160A PRO* 1.3 77.3 - - - +
162A ARG* 1.3 64.6 + - - +
164A LEU* 2.9 22.1 + - + +
165A SER 3.4 2.6 + - - -
195A VAL* 5.6 0.3 - - - +
199A LEU* 4.1 38.9 - - + +
204A HIS* 5.7 3.1 - - - -
205A LEU* 5.7 2.0 - - + -
240A GLN* 4.3 26.0 - - - +
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Residues in contact with ARG 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL 5.2 0.2 - - - -
58A TYR* 3.1 47.3 + - + +
60A VAL* 4.6 1.8 - - - +
155A PHE* 3.9 34.8 - - + -
159A PRO* 2.9 40.5 + - - +
160A PRO 2.9 0.2 + - - -
161A CYS* 1.3 74.9 - - - +
163A TRP* 1.3 64.2 + - - +
165A SER* 3.0 7.1 + - - -
166A MET* 2.9 30.2 + - + +
225A LEU* 3.3 30.6 + - - +
226A PRO 2.8 21.6 + - - -
227A LEU* 3.8 31.1 - - + +
228A GLU 5.0 1.0 - - - +
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Residues in contact with TRP 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 3.8 43.1 - + + -
19A PHE* 4.8 4.9 - + - -
20A VAL* 4.0 25.1 - - + -
160A PRO* 2.9 28.7 + - + +
162A ARG* 1.3 78.1 - - - +
164A LEU* 1.3 67.4 + - - +
166A MET* 3.0 23.0 + - - +
167A SER* 3.0 22.3 + - - -
227A LEU* 3.5 36.9 - - + +
228A GLU 3.3 24.8 + - - -
229A GLU* 4.5 11.7 - - + -
230A PRO* 4.1 22.5 - - + +
237A LEU* 4.5 19.5 - - + -
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A PRO 4.3 0.2 + - - -
161A CYS* 2.9 12.0 + - + +
163A TRP* 1.3 80.5 - - - +
165A SER* 1.3 67.8 + - - +
167A SER* 3.0 12.9 + - - -
168A ILE* 3.1 27.8 + - + +
195A VAL* 4.4 18.4 - - + -
198A TYR* 4.3 24.7 - - + -
199A LEU* 4.5 9.4 - - + -
237A LEU* 4.2 9.9 - - + +
240A GLN* 4.0 28.0 + - + +
241A VAL* 3.7 37.7 - - + +
244A PHE* 4.9 7.2 - - + -
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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
----------------------------------------------------------
58A TYR* 2.8 17.1 + - - -
155A PHE* 3.8 24.4 - - - -
161A CYS 3.4 1.2 + - - -
162A ARG 3.0 8.8 + - - -
164A LEU* 1.3 80.1 - - - +
166A MET* 1.3 69.1 + - - +
168A ILE* 3.0 10.8 + - - +
169A LYS* 3.0 11.3 + - - +
192A ASN* 2.7 27.9 + - - -
195A VAL* 4.3 20.7 - - - +
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Residues in contact with MET 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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16A PHE* 4.5 14.8 - - + -
19A PHE* 4.9 6.7 - - + -
58A TYR* 3.8 36.3 - - + -
60A VAL* 3.8 21.5 - - + -
62A GLU* 4.4 20.5 - - + +
162A ARG* 2.9 20.8 + - + +
163A TRP* 3.3 32.5 - - - +
165A SER* 1.3 77.5 - - - +
167A SER* 1.3 67.5 + - - +
169A LYS* 3.0 12.5 + - - +
170A ARG* 3.0 12.9 + - - +
227A LEU* 3.7 26.5 - - + -
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Residues in contact with SER 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.2 11.1 - - - +
16A PHE* 3.7 25.4 - - - -
163A TRP 3.0 12.8 + - - -
164A LEU* 3.0 11.6 + - - -
166A MET* 1.3 76.7 - - - +
168A ILE* 1.3 66.4 + - - +
170A ARG* 3.0 9.8 + - - +
171A TRP* 2.8 22.6 + - - +
237A LEU* 4.7 7.6 - - - +
241A VAL* 5.3 3.6 - - - -
329A LEU* 3.8 22.4 - - - +
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Residues in contact with ILE 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU* 3.6 26.5 - - + +
165A SER* 3.0 7.7 + - - +
167A SER* 1.3 73.8 - - - +
169A LYS* 1.3 54.6 + - - +
171A TRP* 3.0 21.3 + - + +
172A SER* 2.7 33.1 + - - -
191A PHE* 3.9 31.9 - - + -
195A VAL* 4.4 18.4 - - + -
241A VAL* 5.4 3.1 - - + -
244A PHE* 4.1 30.1 - - + -
245A LEU* 5.7 1.1 - - + -
329A LEU* 4.3 25.8 - - + -
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Residues in contact with LYS 169 (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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54A SER* 3.8 18.9 + - - -
58A TYR* 3.6 23.0 - - - +
62A GLU* 3.0 33.9 + - - +
65A SER* 4.6 6.8 + - - +
165A SER* 3.0 9.3 + - - +
166A MET* 3.0 10.8 + - - +
168A ILE* 1.3 75.8 - - - +
170A ARG* 1.3 65.5 + - - +
172A SER* 2.6 26.9 + - - +
173A LYS* 3.1 31.0 + - + +
188A SER* 3.9 30.1 - - - +
191A PHE* 5.6 5.8 - - + +
192A ASN* 5.7 4.3 - - - +
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Residues in contact with ARG 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.3 6.9 - - - +
15A SER* 3.3 38.6 + - - -
16A PHE* 3.6 41.4 - - + -
166A MET 3.0 9.1 + - - +
167A SER* 3.0 12.6 + - - +
169A LYS* 1.3 76.9 - - - +
171A TRP* 1.3 63.6 + - - +
173A LYS* 2.9 19.9 + - - +
174A GLN* 3.0 31.2 + - + +
329A LEU* 5.6 2.0 + - - +
331A THR* 4.3 15.0 - - - +
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Residues in contact with TRP 171 (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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167A SER 2.8 11.9 + - - +
168A ILE* 3.3 29.6 - - + +
170A ARG* 1.3 76.1 - - - +
172A SER* 1.3 75.1 + - - +
174A GLN* 2.9 21.3 + - - +
175A THR* 3.1 39.3 + - + +
177A LEU* 3.6 24.0 - - + -
191A PHE* 4.6 8.5 - + - -
244A PHE* 5.8 1.8 - + - -
245A LEU* 5.1 2.2 - - + -
317A LEU* 5.1 0.4 - - + -
320A HIS* 3.7 34.4 + - + +
321A LEU* 3.9 26.9 - - + -
324A ALA* 4.0 15.9 - - + +
329A LEU* 3.6 53.3 - - + +
330A LEU* 4.5 6.6 - - + +
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Residues in contact with SER 172 (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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168A ILE 2.7 16.0 + - - -
169A LYS* 2.6 23.1 + - - -
171A TRP* 1.3 78.6 - - - +
173A LYS* 1.3 57.4 + - - +
175A THR* 3.6 6.9 + - - -
176A GLY 3.6 0.2 + - - -
177A LEU* 3.1 13.6 + - - -
178A ASN* 3.0 42.2 + - - -
191A PHE* 3.6 38.6 - - - -
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Residues in contact with LYS 173 (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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64A GLY 5.2 5.7 + - - -
65A SER* 5.0 9.1 + - - +
169A LYS* 3.9 30.5 - - + +
170A ARG* 2.9 11.6 + - - +
172A SER* 1.3 80.5 + - - +
174A GLN* 1.3 60.7 + - + +
175A THR 3.4 0.2 - - - -
176A GLY 4.0 2.5 + - - -
178A ASN* 3.7 36.6 - - + +
180A SER* 4.0 14.1 - - - +
181A VAL* 4.0 18.4 - - + +
188A SER* 4.0 8.0 + - - -
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Residues in contact with GLN 174 (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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170A ARG* 3.0 26.7 + - + +
171A TRP* 2.9 14.9 + - - +
173A LYS* 1.3 80.1 - - - +
175A THR* 1.3 59.2 + - - +
176A GLY 3.5 0.2 - - - -
329A LEU 4.1 6.6 - - - +
330A LEU* 4.0 39.0 + - + +
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Residues in contact with THR 175 (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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171A TRP* 3.2 40.1 + - + +
172A SER 3.6 2.1 + - - -
174A GLN* 1.3 75.9 - - - +
176A GLY* 1.3 59.9 + - - +
177A LEU* 3.3 25.2 + - - +
320A HIS* 3.6 45.1 + - + +
330A LEU* 3.6 21.3 - - + -
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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
------------------------------------------------------------
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