Contacts of the strand formed by residues 507 - 517 (chain B) in PDB entry 6ZGI
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 507 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401B VAL* 4.4 4.9 - - + -
402B ILE 3.6 6.3 - - - +
437B ASN* 3.7 4.0 - - - +
438B SER* 3.2 40.2 + - - +
439B ASN* 3.6 17.0 - - - +
442B ASP* 3.8 20.4 - - + -
443B SER* 3.8 7.6 - - - +
497B PHE* 3.7 35.9 - - + -
498B GLN 5.8 0.7 - - - +
506B GLN* 1.3 90.1 - - + +
508B TYR* 1.3 67.9 + - - +
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Residues in contact with TYR 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B SER* 3.6 25.6 + - - -
401B VAL* 3.3 5.7 - - - -
402B ILE* 2.9 39.5 + - + +
403B ARG 4.7 0.2 - - - +
404B GLY* 3.4 24.5 - - - -
407B VAL* 4.0 29.2 - - + -
435B ALA* 4.8 2.9 - - + -
436B TRP* 3.5 9.2 - - - -
437B ASN* 3.6 47.0 + - + +
438B SER* 4.2 1.6 - - - -
503B VAL* 4.2 20.7 - - - +
506B GLN 3.6 4.5 - - - -
507B PRO* 1.3 87.9 - - - +
509B ARG* 1.3 65.0 + - - +
510B VAL* 4.0 1.9 + - + -
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Residues in contact with ARG 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B PHE 5.2 2.2 + - - -
343B ASN* 5.3 0.8 - - - +
344B ALA 3.0 23.2 + - - +
345B THR 3.6 21.6 + - - -
346B ARG* 4.6 0.2 - - - +
347B PHE* 3.8 34.3 - - + +
400B PHE 3.8 2.5 - - - -
401B VAL* 3.7 17.5 - - + -
435B ALA* 3.3 4.2 - - - -
436B TRP* 2.9 70.8 + - + +
438B SER* 3.7 17.5 + - - +
441B LEU* 3.6 30.9 - - - +
442B ASP* 3.3 29.1 + - - -
451B TYR* 4.7 0.4 + - - -
508B TYR* 1.3 71.9 - - - +
510B VAL* 1.3 60.9 + - - +
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Residues in contact with VAL 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B PHE* 4.1 1.5 - - - -
398B ASP 3.6 0.9 - - - +
399B SER* 3.4 4.7 - - - -
400B PHE* 2.9 58.7 + - + +
402B ILE* 3.8 35.2 - - + -
407B VAL* 4.9 2.0 - - + -
410B ILE* 4.6 6.7 - - + -
433B VAL* 4.5 11.9 - - + -
434B ILE 3.5 9.4 - - - +
435B ALA* 4.0 13.9 - - + -
508B TYR* 4.2 5.2 - - + +
509B ARG* 1.3 78.1 - - - +
511B VAL* 1.3 66.0 + - - +
512B VAL* 4.3 13.9 - - + -
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Residues in contact with VAL 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B VAL* 4.3 24.5 - - + +
342B PHE* 4.4 15.7 - - + -
347B PHE* 4.3 5.4 - - + -
397B ALA* 4.4 3.6 - - + -
398B ASP 3.1 7.9 - - - +
399B SER* 3.9 14.1 - - - +
432B CYS 4.1 0.7 - - - +
433B VAL* 3.8 1.0 - - - -
434B ILE* 2.9 37.9 + - + +
436B TRP* 4.0 24.9 - - + -
510B VAL* 1.3 77.3 - - - +
512B VAL* 1.3 64.7 + - - +
513B LEU* 4.0 26.6 + - + -
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Residues in contact with VAL 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B TYR 3.6 1.2 - - - +
397B ALA* 3.4 2.8 - - - -
398B ASP* 2.9 43.4 + - + +
400B PHE* 4.6 5.8 - - + -
410B ILE* 4.2 24.5 - - + -
423B TYR* 4.0 27.1 - - + +
425B LEU* 4.5 4.3 - - + -
429B PHE* 3.7 31.9 - - + -
432B CYS 3.6 6.5 - - - +
433B VAL* 4.3 9.6 - - + -
464B PHE* 5.6 0.4 - - + -
510B VAL* 4.3 9.6 - - + -
511B VAL* 1.3 76.8 - - - +
513B LEU* 1.3 64.8 + - - +
514B SER* 4.0 1.5 + - - +
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Residues in contact with LEU 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B VAL* 5.5 1.6 - - + -
342B PHE* 4.9 10.8 - - + -
358B ILE* 4.7 10.3 - - + -
377B PHE* 6.3 0.2 - - + -
395B VAL* 5.3 5.8 - - + -
396B TYR 3.4 4.7 - - - +
397B ALA* 3.8 25.6 - - + -
429B PHE* 3.9 3.3 - - - -
431B GLY* 3.1 6.5 - - - -
432B CYS* 2.9 44.7 + - + +
434B ILE* 4.1 26.7 - - + -
511B VAL* 4.0 11.0 - - + -
512B VAL* 1.3 73.7 - - - +
514B SER* 1.3 59.6 + - - +
515B PHE* 4.5 14.8 - - + -
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Residues in contact with SER 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B ARG* 4.7 4.3 + - - -
394B ASN 3.2 5.9 + - - +
395B VAL* 3.3 3.5 - - - +
396B TYR* 2.9 43.2 + - - +
398B ASP* 5.4 4.7 - - - -
429B PHE* 4.3 16.9 - - - -
430B THR 3.9 6.0 + - - -
464B PHE* 4.8 12.7 - - - -
512B VAL* 5.2 2.0 - - - -
513B LEU* 1.3 74.7 - - - +
515B PHE* 1.3 64.4 + - - +
200C TYR* 4.4 12.5 + - - -
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Residues in contact with PHE 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B VAL* 4.4 13.0 - - + -
387B LEU* 4.7 4.0 - - + -
392B PHE* 3.9 37.9 - + + -
393B THR 3.5 13.2 - - - +
394B ASN 3.8 2.7 - - - -
395B VAL* 3.8 20.9 - - + -
430B THR* 3.5 45.3 + - + +
431B GLY* 3.7 20.0 - - - -
432B CYS* 4.4 16.6 - - - -
513B LEU* 4.4 16.6 - - + -
514B SER* 1.3 83.1 + - - +
516B GLU* 1.3 69.0 + - - +
517B LEU* 4.2 11.4 - - + -
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Residues in contact with GLU 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B CYS 4.3 0.2 - - - +
392B PHE* 3.8 1.2 - - - -
393B THR* 2.9 43.3 + - - +
394B ASN* 3.3 28.4 - - - +
430B THR* 5.2 2.9 - - - -
515B PHE* 1.3 77.5 - - - +
517B LEU* 1.3 73.2 + - - +
519B HIS* 6.1 5.4 - - + -
520B ALA* 5.8 0.9 - - - +
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Residues in contact with LEU 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B GLY 4.7 0.9 - - - +
382B VAL* 4.2 20.9 - - + -
390B LEU* 3.9 26.9 - - + -
391B CYS 3.7 11.0 - - - +
392B PHE* 3.6 30.7 - - + -
393B THR* 5.4 0.7 - - - -
430B THR* 4.7 6.0 - - + +
515B PHE* 4.2 11.4 - - + -
516B GLU* 1.3 86.3 - - - +
518B LEU* 1.3 76.3 + - + +
519B HIS* 3.2 22.5 + - - -
983C ARG* 4.3 37.8 + - + +
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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