Contacts of the strand formed by residues 313 - 318 (chain E) in PDB entry 5EIG
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 MET 313 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E GLN* 2.9 30.5 + - - +
190E PHE* 3.9 25.8 - - + -
213E TYR* 3.6 23.1 - - + +
291E TYR* 3.3 13.0 - - - -
311E THR* 3.4 14.4 + - - +
312E GLY* 1.3 75.8 - - - +
314E VAL* 1.3 58.8 + - - +
315E THR* 5.7 0.2 - - - +
341E LEU* 3.5 38.6 - - + -
375E ARG* 3.6 33.2 - - + +
376E LEU 3.4 9.6 - - - +
377E SER* 3.7 17.7 - - - -
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Residues in contact with VAL 314 (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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164E GLN* 4.0 0.2 - - - +
273E GLY* 3.5 26.0 - - - +
276E VAL* 4.3 7.4 - - + -
277E ALA* 4.1 13.9 - - + -
280E LEU* 3.9 27.4 - - + -
289E VAL* 4.1 12.6 - - + -
290E ILE 4.2 1.6 - - - -
291E TYR* 3.6 15.7 - - + -
312E GLY 3.3 7.8 + - - +
313E MET* 1.3 74.8 - - - +
315E THR* 1.3 65.0 + - - +
316E PHE 4.2 0.3 + - - -
374E ILE 4.0 0.3 - - - +
375E ARG* 4.0 0.4 - - - -
376E LEU* 2.8 45.4 + - + +
378E VAL* 4.1 9.6 - - + -
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Residues in contact with THR 315 (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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162E PRO* 2.8 29.8 + - + +
163E THR* 4.8 0.4 - - - -
164E GLN* 3.0 18.1 + - - +
190E PHE* 5.9 0.2 - - - -
289E VAL* 3.7 2.9 - - - +
290E ILE* 2.6 54.5 + - + +
314E VAL* 1.3 72.7 - - - +
316E PHE* 1.3 61.6 + - - +
373E LEU* 3.4 30.5 - - + -
374E ILE 3.5 9.4 - - - +
375E ARG* 4.2 12.7 - - - +
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Residues in contact with PHE 316 (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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280E LEU* 3.6 23.8 - - + -
286E VAL* 3.6 30.1 - - + -
288E LYS 3.2 13.2 - - - +
289E VAL* 4.0 13.5 - - + +
290E ILE 4.5 0.7 - - - +
314E VAL 4.6 0.2 - - - -
315E THR* 1.3 79.0 - - - +
317E TYR* 1.3 68.4 + - - +
318E ILE* 4.1 14.4 - - + -
328E PHE* 3.8 17.9 - + - -
372E THR 3.7 0.2 - - - +
373E LEU* 3.7 2.7 - - - +
374E ILE* 2.9 81.0 + - + +
376E LEU* 3.9 23.8 - - + -
394E LEU* 4.7 2.7 - - + -
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Residues in contact with TYR 317 (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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163E THR* 5.0 3.5 - - - +
286E VAL* 3.4 6.9 - - - +
287E GLU* 2.8 41.3 + - + -
288E LYS* 2.8 36.9 + - + +
290E ILE* 4.0 22.3 - - + +
316E PHE* 1.3 76.1 - - - +
318E ILE* 1.3 62.5 + - - +
367E LEU 5.0 0.9 + - - -
368E GLY* 2.6 37.0 + - - -
370E SER* 3.5 20.4 - - - -
372E THR* 3.4 12.3 - - - +
373E LEU* 3.4 28.4 - - + +
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Residues in contact with ILE 318 (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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285E TRP 3.6 14.1 - - - +
287E GLU* 4.5 3.1 - - - +
316E PHE* 4.0 13.4 + - + -
317E TYR* 1.3 76.9 - - - +
319E LYS* 1.3 75.4 + - - +
320E GLY 3.7 0.9 + - - -
324E HIS* 3.7 26.0 - - + +
325E ALA* 4.0 26.5 - - + +
328E PHE* 3.8 19.7 - - + -
372E THR* 3.1 38.1 + - + +
374E ILE* 4.2 4.7 - - + -
394E LEU* 3.9 18.6 - - + -
397E ALA* 4.4 7.6 - - + -
398E HIS* 4.6 2.9 - - + +
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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