Contacts of the strand formed by residues 373 - 377 (chain G) 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 LEU 373 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162G PRO* 4.2 10.5 - - + -
163G THR* 4.4 13.5 - - + -
290G ILE* 5.3 0.7 - - + -
315G THR* 3.7 28.7 - - + -
316G PHE 3.7 4.3 - - - +
317G TYR* 3.3 40.8 - - + +
350G LEU* 3.8 10.6 - - - +
351G PRO* 3.3 43.3 - - + +
368G GLY 3.3 10.8 - - - +
369G ILE* 4.0 8.7 - - + -
370G SER* 3.4 17.2 + - - +
372G THR* 1.3 78.2 + - - +
374G ILE* 1.3 65.7 + - - +
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Residues in contact with ILE 374 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315G THR* 3.4 3.3 - - - +
316G PHE* 2.8 69.6 + - + +
318G ILE* 4.3 9.6 - - + -
325G ALA* 4.3 24.0 - - + +
328G PHE* 3.5 34.1 - - + -
329G LEU* 4.3 9.9 - - + -
349G GLU 3.4 14.1 - - - +
350G LEU* 4.9 4.5 - - + -
372G THR 4.0 6.5 - - - +
373G LEU* 1.3 81.0 - - - +
375G ARG* 1.3 63.3 + - - +
376G LEU* 3.9 15.5 - - + -
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Residues in contact with ARG 375 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161G ASN* 2.8 49.2 + - - +
162G PRO* 3.9 10.8 - - + -
190G PHE* 4.5 3.4 - - + -
212G 5OW 2.8 30.1 + - - -
313G MET* 3.7 24.1 - - + +
314G VAL 3.9 2.2 - - - +
315G THR* 4.2 14.8 - - - +
339G VAL* 4.7 0.6 - - - +
340G SER 3.6 14.1 + - - +
341G LEU* 3.4 17.0 - - - +
347G LEU 4.1 0.5 - - - +
348G ALA* 3.7 2.4 - - - -
349G GLU* 3.0 66.1 + - - +
351G PRO* 3.9 11.9 - - + +
355G THR* 3.6 9.7 + - - +
373G LEU* 5.1 0.4 - - + -
374G ILE* 1.3 72.2 - - - +
376G LEU* 1.3 65.4 + - - +
377G SER* 5.8 1.0 - - - +
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Residues in contact with LEU 376 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G VAL* 4.0 12.1 - - + -
280G LEU* 3.8 17.9 - - + -
312G GLY 3.5 0.2 - - - +
313G MET* 3.4 12.3 - - - +
314G VAL* 2.7 45.8 + - + +
316G PHE* 3.6 27.4 - - + -
328G PHE* 4.8 5.8 - - + -
335G PHE* 4.3 15.5 - - + -
347G LEU 3.5 3.1 - - - +
348G ALA* 3.7 27.8 - - + -
374G ILE* 3.9 13.0 - - + -
375G ARG* 1.3 77.2 - - - +
377G SER* 1.3 59.6 + - - +
378G VAL* 3.7 3.1 - - + -
390G LEU* 4.0 19.1 - - + -
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Residues in contact with SER 377 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213G TYR* 4.8 1.4 + - - -
269G HIS* 5.8 0.5 - - - -
312G GLY 3.8 2.2 - - - -
313G MET* 3.8 8.8 - - - -
335G PHE* 4.8 0.4 - - - -
340G SER 4.5 1.1 - - - -
341G LEU* 3.4 24.5 - - - +
342G GLY* 3.1 26.5 + - - -
343G GLY 4.5 2.9 + - - -
345G GLU 3.9 3.6 + - - +
346G SER* 3.1 4.9 - - - -
347G LEU* 2.8 44.1 + - - +
375G ARG* 4.2 1.3 + - - +
376G LEU* 1.3 71.8 - - - +
378G VAL* 1.3 64.4 + - - +
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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