Contacts of the helix formed by residues 238 - 255 (chain A) in PDB entry 3C3K
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 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A ILE* 4.0 12.1 - - + -
236A GLN* 4.4 2.0 - - + +
237A GLN* 1.3 85.7 - - + +
239A SER* 1.3 61.6 + - - +
240A GLU 3.3 2.7 - - - -
241A GLN* 3.2 14.3 + - + -
242A ILE* 2.9 23.4 + - + +
267A LEU* 4.0 24.0 - - + -
268A PRO* 3.4 27.8 - - + +
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Residues in contact with SER 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 3.0 34.2 - - - -
25A ALA* 3.8 25.6 - - - +
26A VAL* 3.6 12.4 - - - -
220A ASP 4.5 4.0 + - - -
222A VAL* 5.4 2.4 - - - +
237A GLN* 2.9 16.8 + - - +
238A PRO* 1.3 72.5 - - - +
240A GLU* 1.3 63.5 + - - +
242A ILE* 3.3 14.2 + - - +
243A GLY 3.2 15.4 + - - -
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Residues in contact with GLU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 3.7 15.5 + - + +
28A LYS* 3.2 34.4 + - - +
29A GLY* 3.4 15.4 - - - -
32A LYS* 3.6 28.2 + - - +
238A PRO 3.3 0.4 - - - -
239A SER* 1.3 79.7 - - - +
241A GLN* 1.3 60.4 + - - +
243A GLY 3.2 2.6 + - - -
244A MET* 3.1 35.2 + - - +
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Residues in contact with GLN 241 (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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238A PRO* 3.2 20.9 + - + +
240A GLU* 1.3 78.9 - - - +
242A ILE* 1.3 60.7 + - - +
244A MET* 3.6 34.0 - - - +
245A LYS* 2.8 32.9 + - + +
267A LEU* 3.9 14.1 - - + +
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Residues in contact with ILE 242 (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 PHE* 4.3 7.4 - - + -
26A VAL* 4.1 9.0 - - + -
92A CYS* 3.6 22.2 - - - -
93A ALA* 4.4 7.2 - - + +
104A VAL* 3.5 26.8 - - + +
105A SER* 4.7 8.1 - - - -
106A ILE* 4.2 13.9 - - + -
237A GLN* 3.6 23.6 - - - +
238A PRO* 2.9 23.7 + - + +
239A SER* 3.3 16.8 - - - +
241A GLN* 1.3 76.2 - - - +
243A GLY* 1.3 62.4 + - - +
245A LYS 3.6 0.2 + - - -
246A ALA* 3.0 19.1 + - - +
267A LEU* 3.8 20.2 - - + +
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Residues in contact with GLY 243 (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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26A VAL* 3.6 19.3 - - - -
30A ILE* 3.4 35.5 - - - +
239A SER 3.2 3.8 + - - -
240A GLU 3.2 5.6 + - - -
241A GLN 3.2 0.6 - - - -
242A ILE* 1.3 81.0 - - - +
244A MET* 1.3 60.4 + - - +
246A ALA* 3.2 10.8 + - - +
247A VAL* 3.3 11.6 + - - +
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Residues in contact with MET 244 (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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29A GLY* 3.4 15.6 + - - +
32A LYS* 5.0 8.3 - - + -
33A THR* 3.1 27.8 - - + +
36A LYS* 5.6 9.9 - - - -
240A GLU* 3.1 33.4 + - - +
241A GLN* 3.6 40.8 - - - +
243A GLY* 1.3 74.1 - - - +
245A LYS* 1.3 64.2 + - - +
247A VAL* 3.3 5.2 + - - +
248A SER* 3.1 24.3 + - - -
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Residues in contact with LYS 245 (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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104A VAL* 3.9 20.6 - - + -
241A GLN* 2.8 22.1 + - + +
242A ILE 4.1 2.5 - - - +
244A MET* 1.3 78.0 - - - +
246A ALA* 1.3 61.0 + - - +
248A SER* 3.3 12.3 + - - -
249A LEU* 2.9 48.8 + - + +
252A GLU* 5.0 5.5 + - - -
265A HIS* 3.8 30.9 - - + -
267A LEU* 4.6 13.9 - - + -
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Residues in contact with ALA 246 (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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30A ILE* 4.8 0.2 - - + -
69A ILE* 4.0 17.4 - - + +
90A VAL* 3.4 24.9 - - + +
92A CYS* 3.9 16.2 - - - -
104A VAL* 3.8 16.7 - - + +
242A ILE 3.0 15.2 + - - +
243A GLY* 3.2 10.5 + - - +
245A LYS* 1.3 76.0 - - - +
247A VAL* 1.3 59.1 + - - +
249A LEU* 4.6 0.2 - - - -
250A LEU* 3.0 24.1 + - - +
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Residues in contact with VAL 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.6 9.4 - - + -
30A ILE* 3.5 28.7 - - + +
33A THR* 3.8 12.3 - - + -
34A ALA* 3.7 28.7 - - + +
69A ILE* 3.7 18.6 - - + -
243A GLY 3.3 12.3 + - - +
244A MET 3.3 7.1 + - - +
246A ALA* 1.3 74.7 - - - +
248A SER* 1.3 65.6 + - - +
250A LEU* 3.1 6.5 + - + +
251A LEU* 2.9 38.3 + - + +
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Residues in contact with SER 248 (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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33A THR* 4.0 10.2 - - - +
244A MET* 3.1 15.4 + - - +
245A LYS* 3.3 20.2 + - - +
247A VAL* 1.3 77.0 - - - +
249A LEU* 1.3 62.4 + - - +
251A LEU* 3.5 12.3 + - - +
252A GLU* 3.4 27.7 + - - +
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Residues in contact with LEU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL* 3.7 18.2 - - + -
102A SER* 3.8 15.2 + - - +
103A SER 3.8 17.3 - - - +
104A VAL* 4.3 4.3 - - + -
245A LYS* 2.9 46.3 + - + +
248A SER* 1.3 74.8 - - - +
250A LEU* 1.3 64.2 + - - +
252A GLU* 3.4 32.7 - - - +
253A GLN* 3.5 13.5 + - - +
263A VAL* 4.4 5.4 - - + -
265A HIS* 3.5 40.4 - - + +
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Residues in contact with LEU 250 (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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11A LEU* 3.7 40.4 - - + -
67A GLY* 4.0 5.6 - - - -
68A VAL 3.6 14.4 - - - +
69A ILE* 3.9 20.0 - - + -
88A PRO* 3.5 17.3 - - + +
89A TRP* 3.4 33.2 - - - +
90A VAL* 3.5 6.0 - - + +
246A ALA 3.0 14.5 + - - +
247A VAL* 3.1 8.5 + - - +
249A LEU* 1.3 74.5 - - - +
251A LEU* 1.3 61.9 + - + +
253A GLN* 3.0 8.8 + - - +
254A ILE* 2.9 33.3 + - + +
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Residues in contact with LEU 251 (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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11A LEU* 5.8 2.0 - - + -
33A THR* 5.0 0.2 - - + -
37A ASN* 3.4 40.2 - - + +
39A TYR* 3.7 35.9 - - + -
247A VAL* 2.9 33.1 + - + +
248A SER* 3.8 10.8 - - - +
250A LEU* 1.3 74.8 - - + +
252A GLU* 1.3 57.4 + - + +
254A ILE* 3.0 10.3 + - + -
255A HIS* 2.8 57.7 + - + +
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Residues in contact with GLU 252 (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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245A LYS* 5.0 5.0 + - - -
248A SER* 3.4 17.7 + - - +
249A LEU* 3.4 28.8 - - - +
251A LEU* 1.3 78.4 - - - +
253A GLN* 1.3 60.3 + - + +
255A HIS* 3.6 4.5 + - - +
256A SER* 2.7 29.2 + - - +
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Residues in contact with GLN 253 (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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86A ALA 5.0 2.3 - - - +
87A PHE 4.2 2.1 - - - +
88A PRO* 3.4 19.7 - - + +
89A TRP* 2.7 47.9 + - - +
90A VAL* 3.6 15.6 - - - +
102A SER* 4.0 16.8 + - - -
249A LEU 3.5 8.3 + - - +
250A LEU* 3.0 7.5 + - - +
252A GLU* 1.3 74.2 - - + +
254A ILE* 1.3 67.6 + - - +
256A SER 3.1 11.4 + - - -
257A ASP 3.3 25.0 - - - +
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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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7A LYS 5.7 2.7 - - - +
11A LEU* 3.7 30.3 - - + -
39A TYR* 3.4 27.8 - - + +
66A ASP* 3.5 28.7 - - + +
88A PRO* 3.7 11.4 - - + -
250A LEU* 2.9 31.0 + - + +
251A LEU* 3.0 12.8 + - + +
253A GLN* 1.3 73.8 - - - +
255A HIS* 1.3 74.0 + - + +
256A SER 3.5 0.7 + - - -
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Residues in contact with HIS 255 (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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39A TYR* 5.2 3.8 + - - -
251A LEU* 2.8 43.5 + - + +
252A GLU* 4.4 3.3 - - - +
253A GLN 3.2 0.2 - - - -
254A ILE* 1.3 94.2 - - + +
256A SER* 1.3 64.5 + - - +
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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
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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