Contacts of the strand formed by residues 301 - 307 (chain E) in PDB entry 3IKM
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 GLU 301 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114E TRP* 4.0 1.7 + - - -
259E ARG* 2.5 56.5 + - - +
263E TRP* 3.3 9.0 + - + -
288E LYS* 3.7 0.9 - - - -
289E LEU* 3.0 37.9 + - + +
299E LEU* 3.3 3.9 - - - +
300E ILE* 1.3 93.0 - - + +
302E THR* 1.3 73.8 + - - +
303E LEU* 3.3 14.1 - - + +
338E VAL* 2.9 23.7 - - - +
339E ASN 3.6 4.5 - - - -
340E GLY* 3.6 15.4 + - - +
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Residues in contact with THR 302 (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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287E ASN 4.0 6.1 - - - -
288E LYS* 4.8 6.5 - - + -
299E LEU* 3.6 26.9 - - + -
301E GLU* 1.3 80.8 - - - +
303E LEU* 1.3 65.1 + - - +
304E TRP* 4.7 14.1 - - + +
337E SER* 2.7 28.5 + - - +
338E VAL* 3.1 11.3 - - - -
339E ASN* 3.2 18.0 + - - +
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Residues in contact with LEU 303 (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 LEU* 4.8 13.7 - - + +
255E TRP* 4.3 11.0 - - + +
256E LEU* 4.0 27.4 - - + -
259E ARG* 4.1 22.2 - - + -
286E GLY* 4.3 2.1 - - - -
287E ASN* 3.3 35.2 + - + +
289E LEU* 3.5 19.3 - - + -
301E GLU* 3.3 23.1 - - + -
302E THR* 1.3 97.5 - - - +
304E TRP* 1.3 64.0 + - - +
336E LEU* 4.9 1.8 - - + -
337E SER 2.9 6.1 - - - -
338E VAL* 3.8 21.5 - - + -
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Residues in contact with TRP 304 (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 LEU* 3.9 3.8 - - - +
278E CYS* 4.5 0.4 - - + -
279E GLN* 3.1 8.7 - - - -
280E ASP* 2.6 60.1 - - - -
281E GLU* 4.6 12.2 + - + +
283E GLY 4.3 7.0 - - - -
284E ARG 4.7 0.2 - - - -
285E LYS 2.7 35.9 - - - -
286E GLY* 3.2 11.0 - - - -
287E ASN 5.0 3.8 + - - -
288E LYS* 3.9 27.4 - - - +
302E THR* 4.7 16.6 - - - +
303E LEU* 1.3 77.4 - - - +
305E ASN* 1.3 62.2 + - - +
306E LEU* 3.9 22.4 - - + -
336E LEU* 3.2 26.3 - - - +
337E SER* 3.1 25.9 + - - -
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Residues in contact with ASN 305 (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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243E THR* 5.9 0.8 - - - +
248E SER* 4.1 8.3 + - - -
249E ASN* 4.1 23.6 - - - +
252E LEU* 3.8 28.2 - - + +
284E ARG 3.3 25.7 + - - +
285E LYS* 3.7 17.6 + - + +
304E TRP* 1.3 78.0 - - - +
306E LEU* 1.3 58.2 + - - +
307E GLY* 3.3 8.7 + - - -
334E CYS* 3.7 18.0 - - - +
335E VAL 3.6 15.6 - - - +
336E LEU* 5.8 0.9 - - - -
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Residues in contact with LEU 306 (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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186E LEU* 6.1 4.5 - - + -
281E GLU* 4.8 12.1 - - - +
282E GLU 4.2 1.1 - - - +
283E GLY* 2.9 44.1 - - - +
284E ARG 4.3 1.7 + - - -
304E TRP* 3.9 28.0 - - + -
305E ASN* 1.3 69.9 - - - +
307E GLY* 1.3 64.0 + - - +
308E ASP 3.3 2.4 + - - -
309E HIS* 3.9 15.3 + - - +
310E GLU* 3.3 38.1 - - + +
335E VAL* 3.4 28.1 + - + -
336E LEU* 5.4 0.2 - - - +
337E SER* 5.4 10.1 - - - +
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Residues in contact with GLY 307 (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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305E ASN* 3.3 7.9 + - - -
306E LEU* 1.3 77.4 - - - +
308E ASP* 1.3 65.1 + - - +
311E LEU* 5.1 1.4 - - - +
334E CYS* 3.1 33.4 - - - +
335E VAL* 3.3 21.7 + - - +
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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