Contacts of the strand formed by residues 279 - 288 (chain E) in PDB entry 3EI4
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 ARG 279 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252E ILE* 5.0 1.6 + - - +
253E ILE* 5.4 1.0 + - - +
255E GLN* 3.2 56.2 - - - +
256E SER* 4.0 7.9 + - - +
273E LEU 4.3 0.4 - - - -
274E GLY* 3.5 4.5 - - - -
275E ASP* 2.8 64.0 + - + +
277E GLU* 3.7 22.0 + - + +
278E GLY* 1.3 82.3 - - - +
280E LEU* 1.3 64.0 + - - +
281E PHE* 3.7 24.7 - - + -
304E LEU* 3.8 21.7 - - + +
306E GLY 3.8 5.2 - - - +
307E GLU* 4.3 6.3 - - + +
308E THR* 3.8 6.4 - - - +
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Residues in contact with LEU 280 (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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272E LEU* 4.0 25.1 - - + -
273E LEU 3.4 19.1 - - - +
274E GLY 4.2 0.2 - - - +
279E ARG* 1.3 77.0 - - - +
281E PHE* 1.3 57.4 + - - +
304E LEU* 3.7 3.1 - - - +
305E LEU* 2.8 38.5 + - + +
306E GLY 2.8 21.5 + - - +
308E THR* 4.5 19.7 - - + +
314E LEU* 3.7 29.4 - - + -
322E VAL* 5.3 7.0 - - + -
324E VAL* 5.6 1.1 - - + -
334E VAL* 4.9 8.7 - - + -
336E LEU* 4.6 17.5 - - + -
347E VAL* 4.8 9.6 - - + -
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Residues in contact with PHE 281 (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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252E ILE* 3.3 35.4 - - + -
253E ILE* 5.2 4.0 - - + -
256E SER 6.0 0.4 - - - -
258E ILE* 4.9 15.0 - - + -
272E LEU* 3.6 9.5 - - - +
273E LEU* 2.8 55.2 + - + +
275E ASP* 3.7 22.2 - - + -
279E ARG* 3.7 25.1 - - + -
280E LEU* 1.3 75.1 - - - +
282E MET* 1.3 59.5 + - - +
302E VAL* 3.9 21.1 - - + -
303E GLU 3.5 3.6 - - - -
304E LEU* 3.5 39.0 - - + -
305E LEU* 4.0 3.8 - - - -
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Residues in contact with MET 282 (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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264E VAL* 3.9 15.9 - - + -
270E ARG* 3.5 46.7 - - + +
271E TYR 3.6 11.4 - - - +
272E LEU* 4.1 9.9 - - + -
281E PHE* 1.3 73.2 - - - +
283E LEU* 1.3 68.3 + - - +
284E LEU* 5.1 4.7 - - + +
301E ARG 3.7 1.0 - - - +
302E VAL* 3.3 7.6 - - - -
303E GLU* 2.9 35.8 + - + +
305E LEU* 3.6 33.1 - - + +
336E LEU* 4.6 10.1 - - + -
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Residues in contact with LEU 283 (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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220E ILE* 5.3 2.9 - - + -
230E ILE* 4.3 34.3 - - + -
232E ILE* 5.8 0.2 - - + -
237E ILE* 4.0 21.1 - - + -
270E ARG* 3.2 11.1 - - - +
271E TYR* 2.6 61.9 + - + +
273E LEU* 4.3 15.8 - - + +
281E PHE 4.0 0.6 - - - -
282E MET* 1.3 74.9 - - - +
284E LEU* 1.3 63.0 + - - +
285E LEU* 4.2 9.4 - - + -
300E LEU* 5.2 7.4 - - + -
301E ARG 3.8 4.7 - - - +
302E VAL* 4.0 26.7 - - + +
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Residues in contact with LEU 284 (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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269E SER* 4.0 8.7 - - - +
270E ARG* 4.8 11.2 - - + +
282E MET* 5.1 4.7 - - + +
283E LEU* 1.3 75.9 - - - +
285E LEU* 1.3 83.6 + - - +
286E GLU* 3.6 16.0 + - - +
300E LEU* 3.5 6.1 - - - +
301E ARG* 2.8 76.4 + - - +
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Residues in contact with LEU 285 (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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222E VAL* 4.3 17.7 - - + -
226E PHE* 4.5 12.6 - - + -
230E ILE* 3.9 26.5 - - + -
239E TYR* 5.1 4.5 - - + -
268E GLY 3.5 20.0 - - - +
269E SER* 3.1 21.6 + - - +
271E TYR* 4.5 11.4 - - + -
283E LEU* 4.5 8.5 - - + -
284E LEU* 1.3 85.5 - - - +
286E GLU* 1.3 59.3 + - - +
287E LYS* 3.0 17.7 + - - +
297E LEU* 3.8 13.7 - - + -
299E ASP 3.9 0.7 - - - -
300E LEU* 3.8 29.8 - - + -
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Residues in contact with GLU 286 (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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284E LEU* 3.8 23.6 - - - +
285E LEU* 1.3 67.4 - - - +
287E LYS* 1.3 62.4 + - - +
288E GLU 3.5 0.2 + - - -
297E LEU* 3.6 6.8 - - - +
298E LYS* 2.8 49.0 + - + +
299E ASP* 2.9 50.7 + - + +
300E LEU* 4.3 3.1 - - - +
301E ARG* 3.6 21.7 + - + +
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Residues in contact with LYS 287 (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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225E PRO* 6.3 1.6 - - - -
226E PHE* 3.6 31.2 - - + -
267E ASN* 4.2 12.7 - - - +
269E SER* 3.7 22.2 + - - +
285E LEU 3.0 9.0 + - - +
286E GLU* 1.3 72.0 - - - +
288E GLU* 1.3 63.8 + - - +
289E GLU 4.0 2.5 + - - +
295E VAL* 4.9 21.1 - - + -
296E THR 4.2 1.8 - - - -
298E LYS* 4.8 2.1 - - - +
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Residues in contact with GLU 288 (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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286E GLU 3.5 0.2 + - - -
287E LYS* 1.3 74.9 - - - +
289E GLU* 1.3 71.1 + - - +
290E GLN* 3.4 5.2 + - + +
295E VAL* 4.7 1.7 - - - +
296E THR* 2.9 57.4 + - + +
298E LYS* 3.6 45.6 + - + +
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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