Contacts of the strand formed by residues 421 - 426 (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 VAL 421 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377E TYR* 3.2 25.6 - - - +
378E CYS* 4.9 1.4 - - + +
394E GLY* 4.7 17.1 - - - -
395E MET 4.0 10.2 + - - +
398E LYS* 4.1 2.2 - - - +
399E LYS 5.2 2.5 - - - +
400E ILE* 4.9 18.2 - - + +
419E GLY 3.3 4.0 + - - +
420E ALA* 1.3 71.0 - - - +
422E ASN* 1.3 60.5 + - - +
423E THR 4.8 6.5 - - - +
424E ILE* 6.1 2.0 - - + -
435E SER* 5.7 5.4 - - - -
436E THR 4.1 4.7 - - - +
437E SER* 3.6 12.3 - - - +
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Residues in contact with ASN 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377E TYR* 3.1 25.9 - - - +
378E CYS* 4.3 1.1 - - - -
420E ALA 3.2 4.0 + - - -
421E VAL* 1.3 72.4 - - - +
423E THR* 1.3 61.5 + - - +
436E THR 2.6 15.5 + - - +
437E SER* 3.4 8.0 - - - +
438E ASP* 4.4 4.7 - - + +
463E SER* 6.2 0.2 - - - -
464E MET* 3.6 30.1 - - + +
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Residues in contact with THR 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378E CYS* 3.7 11.7 - - - -
421E VAL* 3.6 4.4 - - - +
422E ASN* 1.3 81.7 - - - +
424E ILE* 1.3 63.0 + - - +
435E SER* 3.7 1.6 - - - -
436E THR* 2.9 37.3 + - - +
464E MET* 5.3 5.2 - - - -
467E VAL* 5.5 9.2 - - - -
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Residues in contact with ILE 424 (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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378E CYS* 4.0 12.0 - - + +
380E LYS* 3.6 22.9 - - + +
392E VAL* 5.1 17.7 - - + +
393E ALA 5.3 8.5 - - - +
394E GLY* 6.1 0.4 - - - -
400E ILE* 5.4 8.1 - - + -
421E VAL* 6.1 2.7 - - + -
423E THR* 1.3 77.8 - - - +
425E VAL* 1.3 62.0 - - - +
426E PHE 4.2 0.6 + - - -
433E PHE* 5.7 5.2 - - + -
434E VAL 3.3 9.2 - - - +
435E SER* 4.8 7.9 - - - -
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Residues in contact with VAL 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380E LYS* 5.5 1.6 - - - -
424E ILE* 1.3 73.2 - - - +
426E PHE* 1.3 63.9 + - - +
427E VAL 3.8 0.3 + - - -
433E PHE* 4.5 1.1 - - - -
434E VAL* 2.9 41.6 + - + +
467E VAL* 6.0 7.4 - - + +
468E THR* 6.6 0.2 - - - -
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Residues in contact with PHE 426 (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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380E LYS* 5.9 1.8 - - - +
381E PHE 5.4 0.9 - - - +
383E PRO* 3.6 35.5 - - + +
392E VAL* 5.4 9.2 - - + -
424E ILE 4.2 1.0 - - - -
425E VAL* 1.3 74.1 - - - +
427E VAL* 1.3 63.5 + - - +
430E ASN* 6.1 2.0 - - - -
432E ARG 4.5 2.0 - - - +
433E PHE* 3.7 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