Contacts of the helix formed by residues 245 - 257 (chain C) in PDB entry 1EQB
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 245 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244C GLY* 1.3 76.1 - - - -
246C GLU* 1.3 67.2 + - - +
247C GLU* 3.6 9.8 + - - +
248C LEU* 3.3 23.3 + - - +
249C TYR* 3.2 23.8 + - - -
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Residues in contact with GLU 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C SER* 1.3 72.4 - - - +
247C GLU* 1.3 64.7 + - - +
249C TYR* 3.2 11.3 + - - +
250C LYS* 2.9 23.4 + - - +
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Residues in contact with GLU 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C SER* 3.2 10.2 + - - +
246C GLU* 1.3 78.1 - - - +
248C LEU* 1.3 57.0 + - - +
250C LYS* 3.1 8.4 + - - +
251C LYS* 2.9 41.4 + - - +
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Residues in contact with LEU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C LEU* 3.4 33.2 - - + -
196C TYR* 5.3 7.4 - - + +
221C HIS* 4.2 27.8 - - + +
222C VAL* 4.6 6.3 - - + -
244C GLY* 4.2 18.4 - - - -
245C SER* 3.3 19.2 + - - +
247C GLU* 1.3 77.9 - - - +
249C TYR* 1.3 67.2 + - + +
251C LYS* 3.4 10.1 + - + +
252C LEU* 3.0 36.6 + - + +
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Residues in contact with TYR 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ASP* 2.6 32.2 + - - -
90C TYR* 3.5 42.9 - + + -
241C ALA* 3.6 20.9 - - + -
242C LYS* 3.6 4.2 - - - -
243C GLY 3.5 2.1 + - - -
244C GLY* 2.8 45.1 + - - -
245C SER 3.2 10.7 + - - -
246C GLU* 3.2 11.7 + - - +
248C LEU* 1.3 83.8 - - + +
250C LYS* 1.3 65.7 + - - +
252C LEU* 3.4 5.6 + - + +
253C ASN* 3.0 31.7 + - - +
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Residues in contact with LYS 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C GLU 2.9 13.0 + - - +
247C GLU* 3.1 11.9 + - - +
249C TYR* 1.3 74.1 - - - +
251C LYS* 1.3 67.7 + - + +
253C ASN* 3.2 7.0 + - - +
254C SER* 3.0 28.8 + - - +
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Residues in contact with LYS 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ALA* 3.7 28.8 + - + +
109C LEU* 5.4 4.9 - - + +
196C TYR* 5.7 3.2 + - - -
247C GLU* 2.9 24.3 + - - +
248C LEU* 3.6 13.5 - - + +
249C TYR 3.3 0.2 - - - -
250C LYS* 1.3 77.2 - - + +
252C LEU* 1.3 58.0 + - - +
254C SER* 3.1 7.3 + - - -
255C ALA* 2.8 29.8 + - - +
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Residues in contact with LEU 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C TYR* 3.5 36.3 - - + +
104C ALA 5.0 1.1 - - - +
105C VAL* 4.4 17.7 - - + +
108C ALA* 4.0 17.0 - - + -
109C LEU* 5.2 2.2 - - + -
222C VAL* 4.0 39.3 - - + -
239C ILE* 4.3 10.7 - - + +
241C ALA* 4.7 2.2 - - + -
248C LEU* 3.0 32.6 + - + +
249C TYR* 3.8 7.9 - - + +
250C LYS 3.3 0.4 - - - -
251C LYS* 1.3 76.4 - - - +
253C ASN* 1.3 62.4 + - - +
255C ALA* 3.3 4.6 + - - +
256C VAL* 3.3 26.7 + - - +
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Residues in contact with ASN 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C TYR* 2.6 47.0 + - + +
90C TYR* 2.7 30.7 + - - -
91C ALA 5.4 0.7 - - - +
92C ASN* 3.0 13.1 + - - +
249C TYR* 3.0 24.1 + - - +
250C LYS* 3.2 7.5 + - - +
252C LEU* 1.3 76.9 - - - +
254C SER* 1.3 58.6 + - - +
257C PHE 3.0 19.4 + - - +
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Residues in contact with SER 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C LYS* 3.0 16.7 + - - +
251C LYS* 3.5 6.9 - - - -
253C ASN* 1.3 76.0 - - - +
255C ALA* 1.3 57.3 + - - +
257C PHE 3.2 11.8 - - - -
258C PRO* 3.5 6.0 - - - +
259C GLY* 2.7 33.3 + - - -
133D VAL 5.0 0.3 - - - +
4293D FFO 5.8 0.2 + - - -
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Residues in contact with ALA 255 (chain C).
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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103C PHE* 5.5 0.9 - - - -
104C ALA* 3.4 37.7 - - + +
107C THR* 4.1 10.0 + - - +
108C ALA* 3.4 22.7 - - + -
251C LYS 2.8 8.6 + - - +
252C LEU* 3.6 6.1 - - - +
254C SER* 1.3 77.1 - - - +
256C VAL* 1.3 55.8 - - - +
259C GLY* 3.3 4.6 - - - -
260C GLY* 2.8 27.2 + - - -
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Residues in contact with VAL 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C TYR* 3.6 17.5 - - - +
92C ASN* 3.8 10.1 - - - +
94C GLN* 4.1 19.5 - - + +
95C PRO* 4.1 9.4 - - + -
104C ALA* 3.7 11.4 - - + -
239C ILE* 3.5 32.3 - - + -
252C LEU 3.3 9.0 + - - +
253C ASN 3.9 0.9 - - - +
254C SER 3.2 0.4 - - - -
255C ALA* 1.3 77.7 - - - +
257C PHE* 1.3 60.9 + - + +
260C GLY* 3.8 0.6 - - - -
261C GLN* 3.0 53.5 + - - +
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Residues in contact with PHE 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C GLU* 3.5 37.0 - - + -
58C GLY* 3.5 32.3 - - - -
59C TYR* 4.3 15.7 - + + +
64C TYR* 3.9 15.5 - + - -
94C GLN* 4.8 7.4 - - - +
253C ASN 3.0 17.5 + - - +
254C SER* 3.2 10.7 + - - +
256C VAL* 1.3 83.1 - - + +
258C PRO* 1.3 80.4 - - + +
259C GLY 3.4 0.2 - - - +
261C GLN* 3.2 22.4 - - + +
262C GLY* 3.6 13.0 - - - +
127D LEU* 4.1 6.7 - - + -
4293D FFO 3.5 24.9 - + - -
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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