Contacts of the strand formed by residues 394 - 402 (chain F) in PDB entry 6M17
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 ASN 394 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357F ARG* 3.0 35.1 + - - +
358F ILE 3.4 14.6 - - - +
359F SER* 4.3 6.5 - - - +
392F PHE* 3.8 2.8 - - - +
393F THR* 1.3 89.4 - - - +
395F VAL* 1.3 64.3 + - - +
396F TYR* 3.7 20.7 + - + -
515F PHE* 3.6 2.6 - - - -
516F GLU* 2.9 51.2 + - + +
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Residues in contact with VAL 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338F PHE* 6.0 1.6 - - + -
357F ARG 3.6 1.6 - - - -
358F ILE* 2.9 51.8 + - + +
359F SER* 5.6 0.2 - - - +
365F TYR* 4.0 15.5 - - + +
392F PHE* 5.2 6.5 - - + -
394F ASN* 1.3 77.5 - - - +
396F TYR* 1.3 76.6 + - - +
513F LEU* 3.9 19.7 - - + -
514F SER 3.6 4.5 - - - +
515F PHE* 3.7 32.8 - - + -
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Residues in contact with TYR 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355F ARG* 3.6 47.6 - - + +
356F LYS 3.5 3.4 - - - +
357F ARG* 3.1 54.1 + - + -
358F ILE* 5.2 0.2 - - - -
394F ASN* 3.7 15.9 + - + -
395F VAL* 1.3 80.3 - - - +
397F ALA* 1.3 61.8 + - - +
398F ASP* 4.2 1.1 - - - +
512F VAL 3.6 0.7 - - - +
513F LEU* 3.3 4.0 - - - -
514F SER* 2.9 48.7 + - - +
516F GLU* 3.5 33.8 + - + -
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Residues in contact with ALA 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341F VAL* 3.8 28.7 - - + -
354F ASN* 5.6 0.2 - - - +
355F ARG* 3.7 0.9 + - - -
356F LYS* 2.8 40.4 + - + +
358F ILE* 4.5 10.5 - - + +
396F TYR* 1.3 74.5 - - - +
398F ASP* 1.3 64.7 + - - +
399F SER* 4.2 3.3 + - - -
511F VAL* 4.7 5.8 - - + -
512F VAL 3.5 4.7 - - - +
513F LEU* 4.2 15.7 - - + -
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Residues in contact with ASP 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353F TRP* 3.9 14.0 - - + -
354F ASN 3.5 10.5 - - - +
355F ARG* 3.1 38.8 + - - -
396F TYR* 4.3 0.6 - - - +
397F ALA* 1.3 79.5 + - - +
399F SER* 1.3 64.4 + - - +
400F PHE* 4.5 5.0 - - + -
423F TYR* 2.5 38.1 + - + +
464F PHE* 4.0 3.3 - - - -
510F VAL 3.8 0.5 - - - +
511F VAL* 3.2 7.1 - - - +
512F VAL* 2.9 37.7 + - + +
514F SER* 5.7 1.1 - - - -
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Residues in contact with SER 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341F VAL* 4.5 12.7 + - - +
347F PHE* 4.0 20.4 - - - -
348F ALA* 3.9 6.2 - - - +
353F TRP* 3.6 0.7 - - - -
354F ASN* 3.1 41.3 + - - +
356F LYS* 6.0 0.7 - - - +
397F ALA 4.3 5.4 + - - -
398F ASP* 1.3 79.8 + - - +
400F PHE* 1.3 69.6 + - - +
510F VAL 3.4 4.7 - - - -
511F VAL* 4.3 8.0 - - - +
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Residues in contact with PHE 400 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347F PHE* 3.2 11.3 - - - -
348F ALA 3.1 9.9 - - - -
349F SER 3.1 20.6 - - - +
350F VAL* 3.9 20.2 - - + -
353F TRP* 3.7 15.5 - + + -
398F ASP* 4.7 2.5 - - + -
399F SER* 1.3 86.3 - - - +
401F VAL* 1.3 66.0 + - - +
402F ILE* 4.1 12.3 - - + -
410F ILE* 4.0 20.2 - - + -
423F TYR* 4.0 42.6 - + + -
510F VAL* 3.0 53.6 + - + -
512F VAL* 4.5 9.2 - - + -
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Residues in contact with VAL 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347F PHE* 3.6 25.6 - - + -
348F ALA 3.3 3.6 + - - +
350F VAL* 3.6 15.8 + - - +
400F PHE* 1.3 81.0 - - - +
402F ILE* 1.3 76.1 + - - +
442F ASP* 4.3 3.6 - - - +
451F TYR* 4.0 40.2 - - + +
495F TYR* 4.4 5.9 - - - -
497F PHE* 4.5 5.2 - - + -
507F PRO* 4.2 17.3 - - + -
508F TYR 3.4 8.7 - - - +
509F ARG* 3.6 17.5 - - + -
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Residues in contact with ILE 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350F VAL* 3.2 35.0 - - + -
400F PHE* 4.1 6.3 - - + -
401F VAL* 1.3 73.8 - - - +
403F ARG* 1.3 70.3 + - - +
406F GLU* 3.7 43.3 - - - +
407F VAL* 4.1 8.7 - - + -
410F ILE* 4.2 12.8 - - + -
418F ILE* 4.2 6.5 - - + -
495F TYR* 4.3 6.1 - - - +
497F PHE* 4.5 5.6 - - - -
507F PRO* 3.5 6.2 - - - +
508F TYR 2.9 27.2 + - - +
510F VAL* 3.7 29.6 - - + -
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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