Contacts of the helix formed by residues 248 - 260 (chain A) in PDB entry 3ELP
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
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Residue Dist Surf HB Arom Phob DC
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247A PRO* 1.3 74.4 - - - +
249A PRO* 1.3 74.8 - - - +
250A ILE* 3.0 21.9 + - - +
251A ASP* 3.0 32.4 + - - -
252A CYS* 3.1 13.2 + - - -
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Residues in contact with PRO 249 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A GLY 5.0 11.2 - - - +
67A THR* 3.3 31.6 - - + +
247A PRO 4.5 1.8 - - - +
248A SER* 1.3 86.3 - - - +
250A ILE* 1.3 64.2 + - + +
252A CYS* 4.5 2.2 - - + -
253A TYR* 3.0 20.8 + - - +
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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
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248A SER* 3.0 10.4 + - - +
249A PRO* 1.3 78.2 - - + +
251A ASP* 1.3 69.8 + - - +
253A TYR* 3.0 8.5 + - + +
254A LEU* 2.8 47.4 + - + +
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Residues in contact with ASP 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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219A ASP 4.5 4.3 - - - +
220A VAL* 3.6 19.7 - - + +
221A VAL* 4.2 15.0 + - - +
222A MET* 3.7 15.5 - - + -
247A PRO* 4.2 5.8 - - + +
248A SER* 3.0 35.4 + - - +
250A ILE* 1.3 79.7 - - - +
252A CYS* 1.3 54.0 + - - +
254A LEU* 4.5 3.4 - - - +
255A CYS* 2.7 37.2 + - - +
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Residues in contact with CYS 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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67A THR* 3.8 20.2 - - + +
68A ARG* 3.8 34.5 - - - +
71A LEU* 3.8 25.8 - - + +
222A MET* 3.9 0.2 - - - -
247A PRO* 3.9 19.5 - - - -
248A SER 3.1 14.5 + - - +
249A PRO* 3.7 8.5 - - - +
251A ASP* 1.3 79.1 - - - +
253A TYR* 1.3 59.8 + - - +
255A CYS* 3.8 0.9 - - - +
256A ASN* 2.9 31.9 + - - +
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Residues in contact with TYR 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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67A THR* 3.9 13.7 - - + -
249A PRO 3.0 19.1 + - - +
250A ILE* 3.4 9.0 - - + +
252A CYS* 1.3 79.1 - - - +
254A LEU* 1.3 76.8 + - + +
256A ASN* 3.6 6.3 - - + +
257A ARG* 2.9 54.3 + - + +
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Residues in contact with LEU 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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215A ASN* 4.8 3.6 + - - -
218A SER* 4.9 6.2 + - - +
219A ASP 5.8 0.9 - - - +
220A VAL* 3.4 30.1 - - + -
250A ILE* 2.8 41.9 + - + +
251A ASP* 3.7 2.5 - - - +
253A TYR* 1.3 95.7 - - + +
255A CYS* 1.3 64.7 + - - +
257A ARG* 3.1 8.3 + - + +
258A GLY* 3.0 20.1 + - - -
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Residues in contact with CYS 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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71A LEU* 3.9 14.6 - - + -
208A TYR* 6.5 0.2 - - - -
210A ALA* 5.7 5.8 - - - -
220A VAL* 3.9 11.2 - - + +
222A MET* 3.4 37.7 - - + -
224A LEU* 4.5 9.2 - - - -
251A ASP 2.7 20.9 + - - +
252A CYS 3.8 2.7 - - - +
254A LEU* 1.3 73.5 - - - +
256A ASN* 1.3 63.3 + - - +
258A GLY* 3.1 11.5 + - - -
259A LEU* 3.1 27.0 + - - +
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Residues in contact with ASN 256 (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 ALA 4.6 6.3 + - - -
25A VAL 5.2 0.2 + - - -
27A GLN* 3.3 28.7 + - - +
67A THR 5.0 1.1 - - - +
70A CYS* 3.9 8.1 - - - +
71A LEU* 3.6 36.1 + - + +
74A ALA* 4.6 7.7 - - - +
252A CYS 2.9 18.9 + - - +
253A TYR* 3.6 7.2 - - + +
255A CYS* 1.3 76.8 - - - +
257A ARG* 1.3 63.7 + - - +
259A LEU* 3.2 24.0 + - - +
260A LYS* 3.7 14.1 + - - +
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Residues in contact with ARG 257 (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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215A ASN* 5.2 5.4 - - - +
253A TYR* 2.9 42.5 + - + +
254A LEU* 3.1 15.9 + - + +
256A ASN* 1.3 76.5 - - - +
258A GLY* 1.3 62.0 + - - +
260A LYS* 3.3 33.9 - - - +
261A THR* 4.8 1.0 + - - +
215B ASN* 2.5 49.5 + - - +
216B GLY* 4.1 7.7 - - - -
217B HIS 5.0 3.4 - - - +
218B SER* 3.7 14.4 + - - +
344B PHE* 4.9 10.0 - - - -
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Residues in contact with GLY 258 (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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215A ASN* 3.4 32.1 - - - +
254A LEU 3.0 11.6 + - - -
255A CYS* 3.1 4.8 + - - -
257A ARG* 1.3 76.1 - - - +
259A LEU* 1.3 63.7 + - - +
261A THR* 3.3 11.4 + - - -
265A ARG* 2.9 25.0 + - - -
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Residues in contact with LEU 259 (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 ALA* 3.9 15.7 - - - +
71A LEU* 4.2 14.8 - - + -
74A ALA* 5.0 4.0 - - + -
75A VAL* 3.8 30.7 - - + +
78A LEU* 4.1 24.7 - - + -
208A TYR* 5.3 12.1 - - + -
224A LEU* 5.6 2.2 - - + -
255A CYS* 3.1 25.5 + - - +
256A ASN* 3.2 17.7 + - - +
258A GLY* 1.3 75.1 - - - +
260A LYS* 1.3 67.2 + - - +
262A LEU* 2.8 36.0 + - + +
263A HIS 4.6 0.7 + - - -
265A ARG* 6.0 0.7 - - - +
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Residues in contact with LYS 260 (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 ALA* 3.1 28.0 + - - +
23A ILE* 3.4 41.2 + - + +
27A GLN* 3.3 33.3 + - - +
256A ASN* 3.8 11.4 + - - +
257A ARG* 3.3 30.6 - - - +
258A GLY 3.2 0.2 - - - -
259A LEU* 1.3 77.4 - - - +
261A THR* 1.3 58.4 + - - +
263A HIS* 3.2 23.0 + - - -
344B PHE* 3.6 30.5 - - + -
380B LEU* 5.4 0.9 - - - +
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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