Contacts of the helix formed by residues 248 - 265 (chain A) in PDB entry 1CL8
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 SER 248 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ALA* 3.3 32.8 - - - +
29A LYS* 4.3 2.0 - - - +
32A ASP* 3.4 13.5 + - - -
33A LEU* 2.8 34.3 + - - -
38A VAL* 4.6 3.6 - - - +
246A TRP 3.6 3.7 + - - -
247A ASP* 1.3 73.8 + - - +
249A LYS* 1.3 63.8 + - - +
251A MET* 3.6 13.8 - - - +
252A PHE* 3.0 23.7 + - - +
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Residues in contact with LYS 249 (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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22A GLY 5.7 0.9 - - - -
25A GLY* 3.5 30.9 + - - +
26A ASP* 4.0 20.8 + - - +
29A LYS* 3.9 33.0 - - + +
247A ASP* 3.1 14.9 + - - +
248A SER* 1.3 77.5 - - - +
250A ILE* 1.3 66.0 + - + +
252A PHE* 3.4 5.8 + - - +
253A GLU* 3.2 39.4 + - - +
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Residues in contact with ILE 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A GLN* 4.5 7.0 - - - +
246A TRP* 3.5 31.0 - - + -
247A ASP* 3.0 38.6 - - + +
249A LYS* 1.3 79.2 - - + +
251A MET* 1.3 64.7 + - - +
253A GLU* 3.4 19.2 + - - +
254A ILE* 3.0 34.6 + - + +
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Residues in contact with MET 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU 3.8 22.7 - - - +
34A ALA* 5.1 0.2 - - - -
35A VAL* 4.4 15.7 - - - +
38A VAL* 4.1 10.3 - - + -
112A ALA* 5.8 1.8 - - - -
168A PHE* 4.0 28.7 - - + -
246A TRP* 3.8 37.9 - - + +
247A ASP 3.1 14.7 + - - +
248A SER* 3.6 19.5 - - - +
249A LYS 3.3 0.2 - - - -
250A ILE* 1.3 75.8 - - - +
252A PHE* 1.3 56.9 + - - +
254A ILE* 3.4 2.3 + - - +
255A MET* 3.0 49.8 + - + +
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Residues in contact with PHE 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 3.6 35.2 - - + -
24A PHE* 3.5 19.1 - - + -
25A GLY* 3.9 14.8 - - - -
28A ALA* 4.7 5.4 - - + -
38A VAL* 3.6 15.9 - - + +
41A LEU* 3.8 41.1 - - + -
42A VAL* 3.7 22.7 - - + -
45A ALA* 3.9 14.6 - - + -
248A SER 3.0 13.7 + - - +
249A LYS* 3.5 9.9 - - - +
251A MET* 1.3 77.6 - - - +
253A GLU* 1.3 63.3 + - + +
255A MET* 3.4 1.4 + - - +
256A PHE* 2.9 42.1 + + + +
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Residues in contact with GLU 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER* 3.2 23.7 + - - +
21A ILE* 4.8 11.3 - - + +
25A GLY* 5.7 0.4 - - - -
249A LYS* 3.2 24.8 + - + +
250A ILE* 3.7 26.7 - - - +
251A MET 3.4 0.2 - - - -
252A PHE* 1.3 85.7 - - + +
254A ILE* 1.3 59.5 + - + +
256A PHE* 4.0 4.7 - - - +
257A ASP* 3.1 29.1 + - - +
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Residues in contact with ILE 254 (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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166A VAL* 4.3 5.6 - - + -
168A PHE* 4.0 24.7 - - + -
238A TYR* 3.4 58.6 - - + +
246A TRP* 4.1 14.1 - - + -
250A ILE* 3.0 24.2 + - + +
251A MET 3.7 4.0 - - - +
253A GLU* 1.3 77.3 - - + +
255A MET* 1.3 61.4 + - - +
257A ASP* 3.4 7.1 + - - +
258A ILE* 3.2 25.7 + - + +
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Residues in contact with MET 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 4.0 11.0 - - + -
38A VAL* 3.5 28.9 - - + -
39A SER* 4.1 13.0 - - - -
42A VAL* 4.0 7.9 - - + -
108A LEU* 3.9 24.7 - - + +
110A ALA* 3.9 22.9 - - + -
166A VAL* 4.7 3.4 - - + -
168A PHE* 3.5 30.1 - - + -
251A MET* 3.0 36.0 + - + +
252A PHE 3.9 2.9 - - - +
254A ILE* 1.3 73.2 - - - +
256A PHE* 1.3 59.8 + - - +
258A ILE* 3.4 5.2 + - - +
259A SER* 3.0 32.4 + - - -
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Residues in contact with PHE 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 5.4 3.4 - - - -
21A ILE* 3.5 39.3 - - + -
42A VAL* 4.1 20.1 - - + +
45A ALA* 3.8 31.6 - - + -
46A LEU* 3.7 20.2 - - + -
49A GLU* 4.1 13.9 - - + -
50A TYR* 5.5 1.1 - + - -
252A PHE* 2.9 29.5 + + + +
253A GLU* 4.0 5.4 - - - +
255A MET* 1.3 73.4 - - - +
257A ASP* 1.3 66.8 + - - +
259A SER* 3.3 2.1 + - - -
260A THR* 3.0 46.9 + - + +
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Residues in contact with ASP 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ASN* 2.9 29.9 + - - +
238A TYR* 5.1 2.8 + - - -
253A GLU 3.1 19.3 + - - +
254A ILE* 3.5 7.8 - - - +
255A MET 3.3 0.2 - - - -
256A PHE* 1.3 80.4 - - - +
258A ILE* 1.3 58.8 + - - +
260A THR* 2.7 23.0 + - - -
261A THR* 2.9 18.5 + - - -
264A ARG* 5.5 3.1 + - - -
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Residues in contact with ILE 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 4.4 2.2 - - + -
164A PRO* 3.8 35.2 - - + +
165A TYR 5.2 0.4 - - - +
166A VAL* 3.3 36.6 - - + -
216A ASN* 3.7 25.8 - - + +
218A CYS* 4.0 10.7 - - + -
236A SER* 3.7 22.9 - - - +
238A TYR* 4.4 2.9 - - + +
254A ILE* 3.2 22.7 + - + +
255A MET 3.9 4.5 - - - +
257A ASP* 1.3 76.5 - - - +
259A SER* 1.3 62.8 + - - +
261A THR* 3.3 3.7 + - - -
262A SER* 3.1 21.1 + - - -
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Residues in contact with SER 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 3.6 8.1 - - - +
46A LEU* 4.0 18.9 - - - +
107A VAL* 3.2 31.1 - - - +
108A LEU* 3.5 26.5 - - - +
255A MET 3.0 20.5 + - - -
256A PHE 3.5 6.5 - - - -
257A ASP 3.2 0.2 - - - -
258A ILE* 1.3 77.2 - - - +
260A THR* 1.3 62.3 + - - +
262A SER 3.2 8.5 + - - -
263A LEU* 3.2 12.5 + - - +
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Residues in contact with THR 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.4 7.9 - - + -
50A TYR* 4.4 17.2 + - + +
256A PHE* 3.0 44.7 + - + +
257A ASP* 2.7 27.0 + - - -
259A SER* 1.3 73.9 - - - +
261A THR* 1.3 64.7 + - - +
263A LEU* 3.2 11.9 + - - +
264A ARG* 3.1 32.4 + - - +
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Residues in contact with THR 261 (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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216A ASN* 3.0 20.1 + - - +
218A CYS* 3.8 16.4 - - + -
219A ILE* 3.7 27.8 - - + -
257A ASP* 2.9 16.9 + - - -
258A ILE 3.5 8.7 - - - -
259A SER 3.2 0.2 - - - -
260A THR* 1.3 76.0 + - - +
262A SER* 1.3 62.7 + - - +
264A ARG* 3.1 46.4 + - - +
265A VAL* 3.2 14.2 + - - +
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Residues in contact with SER 262 (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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107A VAL* 2.9 33.4 + - - -
162A HIS* 3.3 25.0 - - - -
164A PRO* 3.2 14.7 - - - +
218A CYS* 3.4 3.9 - - - -
258A ILE 3.1 11.9 + - - -
259A SER 3.2 10.3 + - - -
261A THR* 1.3 76.6 - - - +
263A LEU* 1.3 56.0 + - - +
265A VAL* 3.4 4.0 + - - +
266A LEU* 3.0 33.0 + - - +
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Residues in contact with LEU 263 (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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46A LEU* 4.2 12.3 - - + -
50A TYR* 3.5 45.1 - - + +
53A LEU* 4.9 1.3 - - + -
55A PHE* 4.3 15.3 - - + -
97A VAL* 4.5 7.6 - - + -
107A VAL* 3.7 29.2 - - + -
259A SER 3.2 15.0 + - - +
260A THR* 3.2 11.4 + - - +
261A THR 3.2 0.6 - - - -
262A SER* 1.3 78.9 - - - +
264A ARG* 1.3 58.9 + - + +
266A LEU* 3.3 5.2 + - + -
267A GLY* 2.8 28.4 + - - -
270A LEU* 4.2 17.2 - - + +
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Residues in contact with ARG 264 (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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216A ASN* 5.4 0.6 - - - +
219A ILE* 4.6 12.0 - - + +
257A ASP* 5.5 3.0 + - - -
260A THR* 3.1 20.8 + - - +
261A THR* 3.1 46.8 + - + +
263A LEU* 1.3 76.8 - - + +
265A VAL* 1.3 62.0 + - + +
267A GLY* 3.3 11.8 + - - -
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Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A SER* 3.8 31.9 - - - +
162A HIS* 3.9 32.1 - - + +
219A ILE* 4.2 26.7 - - + -
261A THR* 3.2 15.5 + - + +
262A SER 3.7 5.4 - - - +
263A LEU 3.3 0.2 - - - -
264A ARG* 1.3 77.5 - - + +
266A LEU* 1.3 62.6 + - + +
267A GLY 3.2 0.9 + - - -
268A ARG* 4.5 16.5 + - - +
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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