Contacts of the strand formed by residues 245 - 251 (chain E) in PDB entry 1AXC
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 GLY 245 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51E THR* 3.1 13.2 + - - -
53E ARG* 3.2 29.7 + - - +
240E LYS* 3.9 8.1 - - - +
241E ILE 3.1 16.0 + - - +
243E ASP 5.3 0.2 + - - -
244E MET* 1.3 83.4 - - - +
246E HIS* 1.3 69.6 + - - +
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Residues in contact with HIS 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E GLN* 2.9 30.3 + - - -
50E LEU* 3.6 5.4 - - - +
51E THR* 2.9 52.0 + - + +
53E ARG* 5.6 2.0 + - - -
238E GLU* 3.2 24.4 + - - +
239E TYR 3.4 12.6 - - - +
240E LYS* 4.1 5.1 - - + +
241E ILE* 3.7 10.3 - - - +
245E GLY* 1.3 76.2 - - - +
247E LEU* 1.3 64.4 + - - +
248E LYS* 3.5 33.2 - - + -
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Residues in contact with LEU 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E VAL* 4.7 8.7 - - + -
18E ALA* 4.2 4.3 - - + -
19E LEU* 3.9 14.8 - - + -
48E VAL* 3.4 34.1 - - + -
49E GLN 3.6 5.6 - - - +
50E LEU* 4.1 12.6 - - + -
218E ALA* 4.1 1.3 - - + -
221E LEU* 3.4 28.3 - - + -
237E VAL 3.9 1.0 - - - +
238E GLU* 3.5 1.0 - - - -
239E TYR* 2.8 44.1 + - + +
241E ILE* 4.2 9.0 - - + -
246E HIS* 1.3 76.1 - - - +
248E LYS* 1.3 61.6 + - - +
249E TYR* 3.5 27.4 - - + +
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Residues in contact with LYS 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E LEU 3.8 0.3 - - - +
48E VAL* 3.2 7.6 - - - +
49E GLN* 2.8 48.5 + - + +
236E VAL* 4.2 13.6 - - + +
237E VAL 3.6 3.6 - - - +
238E GLU* 3.5 38.0 + - + +
246E HIS* 3.5 35.1 - - + +
247E LEU* 1.3 73.4 - - - +
249E TYR* 1.3 62.3 + - - +
250E TYR* 4.1 32.1 + - + +
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Residues in contact with TYR 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ALA* 2.9 29.4 + - - +
22E LEU* 4.1 5.2 - - + -
47E LEU 3.3 5.6 - - - -
48E VAL* 3.8 30.3 - - + -
214E PHE 4.8 0.4 - - - -
215E PHE* 3.3 55.6 + + + -
218E ALA* 3.0 21.3 - - + +
235E LEU 3.6 0.5 - - - +
236E VAL* 3.4 2.1 - - - -
237E VAL* 2.9 44.7 + - - +
239E TYR* 3.5 35.4 - + - -
247E LEU* 3.5 18.5 - - + +
248E LYS* 1.3 74.8 - - - +
250E TYR* 1.3 61.3 + - - +
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Residues in contact with TYR 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E SER* 3.1 9.0 - - - -
47E LEU* 2.7 57.5 + - + +
49E GLN* 4.4 10.3 - - + +
128E ILE* 3.8 33.5 - - + +
133E TYR* 4.1 6.1 + - - -
215E PHE* 3.8 1.0 - - - -
234E PRO* 4.3 7.0 - - + -
235E LEU 3.0 6.3 - - - +
236E VAL* 3.6 33.8 - - + +
248E LYS* 4.1 33.0 + - + +
249E TYR* 1.3 78.7 - - - +
251E LEU* 1.3 59.6 + - - +
147F MET* 3.7 29.8 - - + -
151F TYR* 4.9 3.8 - + - -
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Residues in contact with LEU 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E VAL* 3.5 31.6 - - + +
46E SER* 4.5 1.1 - - - -
207E PHE* 3.4 27.8 - - + -
208E ALA 3.8 12.3 - - - +
211E TYR* 3.7 24.9 - - + -
212E LEU* 3.6 34.5 - - + -
215E PHE* 3.6 13.2 - - + -
234E PRO* 4.0 2.0 - - - -
235E LEU* 2.9 35.4 + - + +
249E TYR 4.2 0.2 + - - -
250E TYR* 1.3 73.8 - - - +
252E ALA* 1.3 72.2 + - - +
144F GLN* 5.0 0.7 - - - +
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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