Contacts of the strand formed by residues 376 - 381 (chain E) in PDB entry 5MQF
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 PRO 376 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336E ARG* 3.4 22.5 - - - +
350E ALA* 3.7 32.0 - - + +
351E ALA 3.7 9.6 - - - +
354E ARG* 3.7 15.9 - - - -
355E TYR 5.0 1.3 - - - +
356E LEU* 5.1 9.9 - - + -
372E ASN* 5.0 7.6 - - + -
374E LYS 3.2 9.2 - - - +
375E VAL* 1.3 84.3 - - + +
377E TYR* 1.3 60.8 + - - +
378E CYS 3.5 5.2 - - - +
393E ALA* 5.5 3.8 - - + -
394E GLY 3.2 13.7 - - - +
395E MET* 3.8 6.7 - - + -
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Residues in contact with TYR 377 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336E ARG* 5.2 4.8 - - - +
337E ASP* 4.8 7.2 - - - +
375E VAL 3.3 3.5 + - - +
376E PRO* 1.3 72.6 - - - +
378E CYS* 1.3 55.1 + - - +
394E GLY 2.5 10.4 + - - +
395E MET* 4.4 10.3 - - - -
396E SER* 4.7 3.4 - - - +
420E ALA* 6.0 2.0 - - + -
421E VAL 3.2 24.5 - - - +
422E ASN* 3.1 16.2 - - - +
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Residues in contact with CYS 378 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337E ASP* 4.2 6.3 - - - +
350E ALA* 5.0 1.3 - - - -
376E PRO* 3.5 5.3 - - - +
377E TYR* 1.3 80.8 - - - +
379E VAL* 1.3 62.2 + - - +
392E VAL 5.7 0.4 - - - +
393E ALA* 3.3 9.4 - - - +
394E GLY* 2.9 36.0 + - - +
421E VAL* 4.9 1.8 - - + +
422E ASN 3.7 2.0 - - - +
423E THR* 3.7 30.3 - - - +
424E ILE* 4.0 11.2 - - + +
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Residues in contact with VAL 379 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337E ASP* 3.7 14.4 - - + +
338E ILE 3.5 16.5 - - - +
339E CYS* 4.0 14.3 - - + +
348E LEU* 5.5 3.8 - - + -
349E SER 5.1 2.0 - - - -
350E ALA* 3.8 25.8 - - + +
378E CYS* 1.3 77.1 - - - +
380E LYS* 1.3 63.0 + - - +
392E VAL 4.0 2.5 - - - -
393E ALA* 4.4 4.9 - - + -
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Residues in contact with LYS 380 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339E CYS* 4.3 6.9 - - - +
378E CYS* 6.3 0.2 - - + -
379E VAL* 1.3 75.5 - - - +
381E PHE* 1.3 66.4 + - - +
391E PHE* 3.4 9.2 - - - +
392E VAL* 2.9 43.0 + - + +
424E ILE 3.6 23.6 - - - +
425E VAL* 5.5 2.0 - - - -
426E PHE 5.9 1.6 - - - +
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Residues in contact with PHE 381 (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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339E CYS* 4.5 5.8 - - + +
340E PHE 3.2 28.7 - - - +
341E ASN* 4.8 6.5 - - - -
342E THR 5.5 0.7 - - - +
380E LYS* 1.3 81.5 - - - +
382E ASN* 1.3 66.4 + - - +
383E PRO* 3.4 9.5 - - - +
388E GLN* 6.3 0.2 - - + -
391E PHE* 4.5 6.1 - - - -
392E VAL* 4.7 4.0 + - - +
426E PHE* 5.4 0.5 - - - +
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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