Contacts of the strand formed by residues 451 - 461 (chain B) in PDB entry 3GZN
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 THR 451 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173B ARG 4.4 6.1 - - - -
174B TRP* 4.1 6.1 - - - +
177B GLY* 3.9 6.2 - - - -
222B GLU* 5.2 5.6 - - - +
397B MET* 5.7 2.5 - - + -
448B ASP* 2.8 28.7 + - + +
449B VAL 3.0 3.2 + - - -
450B THR* 1.3 92.7 - - - +
452B PRO* 1.3 74.4 - - - +
453B GLN* 3.1 36.7 + - - +
455B VAL* 4.5 15.9 - - + -
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Residues in contact with PRO 452 (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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174B TRP* 3.4 52.2 - - + +
177B GLY 4.1 1.3 - - - +
178B MET* 3.7 37.2 - - + +
181B SER* 5.5 3.1 - - - +
451B THR* 1.3 88.8 - - - +
453B GLN* 1.3 60.3 + - + +
454B THR* 4.0 1.4 + - - -
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Residues in contact with GLN 453 (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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177B GLY* 3.5 34.9 - - - +
180B ILE* 3.4 20.9 - - - +
181B SER* 4.2 16.5 + - - -
365B PRO 5.1 1.0 + - - -
366B ALA* 3.3 34.7 + - - +
446B VAL 3.9 4.7 - - - +
447B ALA* 4.6 7.1 - - - +
451B THR* 3.1 21.4 + - + +
452B PRO* 1.3 81.1 - - - +
454B THR* 1.3 68.3 + - - +
455B VAL* 3.6 11.2 + - + +
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Residues in contact with THR 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B ALA* 3.7 31.9 - - + -
446B VAL 3.6 9.2 - - - +
447B ALA* 5.3 5.5 - - + +
452B PRO 4.0 1.6 + - - -
453B GLN* 1.3 74.1 - - - +
455B VAL* 1.3 63.1 + - - +
456B LEU* 3.7 19.5 + - + +
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Residues in contact with VAL 455 (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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365B PRO* 3.4 36.8 - - + +
372B GLN* 4.7 4.9 - - + -
397B MET* 3.7 23.6 - - + -
444B LEU 3.7 1.0 - - - +
445B ALA* 3.8 0.7 - - - -
446B VAL* 2.8 45.9 + - - +
447B ALA* 5.5 0.9 - - - -
448B ASP 6.0 0.2 - - - +
451B THR* 4.5 14.1 - - + -
453B GLN* 4.1 12.8 - - + +
454B THR* 1.3 70.9 - - - +
456B LEU* 1.3 62.8 + - - +
457B PHE* 3.9 22.8 - - + -
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Residues in contact with LEU 456 (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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369B GLN 6.1 0.9 - - - +
371B PRO* 3.2 25.3 - - + +
372B GLN* 2.7 34.5 + - - +
443B GLU* 3.9 33.9 - - - +
444B LEU 3.7 9.4 - - - +
445B ALA* 4.3 7.0 - - + -
454B THR* 3.7 26.4 + - + +
455B VAL* 1.3 74.9 - - - +
457B PHE* 1.3 55.6 + - - +
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Residues in contact with PHE 457 (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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371B PRO* 4.5 0.9 - - - -
372B GLN* 3.3 32.5 - - + -
374B ILE* 3.5 37.5 - - + -
389B LEU* 3.6 26.7 - - + -
395B LEU* 3.7 29.4 - - + -
397B MET* 4.2 6.5 - - + -
443B GLU* 3.1 7.0 - - - +
444B LEU* 2.9 41.2 + - + +
446B VAL* 3.5 39.5 - - + -
455B VAL* 3.9 17.0 - - + -
456B LEU* 1.3 77.0 - - - +
458B LYS* 1.3 61.1 + - - +
459B LEU 4.0 0.2 - - - -
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Residues in contact with LYS 458 (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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371B PRO* 4.3 13.2 - - + +
372B GLN 2.6 12.1 + - - +
373B ASN* 3.4 19.1 - - - +
374B ILE* 3.1 24.0 + - - -
441B GLY* 3.0 39.3 - - - +
442B GLN 3.6 2.9 - - - +
443B GLU* 4.3 5.4 - - + +
457B PHE* 1.3 71.9 - - - +
459B LEU* 1.3 63.1 + - - +
460B HIS* 3.3 22.5 - - + -
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Residues in contact with LEU 459 (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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374B ILE* 3.7 12.5 - - + +
376B PHE* 4.0 36.6 - - + -
385B VAL* 5.6 0.9 - - + -
433B LEU* 4.2 12.3 - - + -
438B LEU* 4.2 26.7 - - + -
439B VAL 4.7 6.1 - - - +
441B GLY* 2.8 33.5 + - - -
442B GLN* 2.7 23.2 + - + +
444B LEU* 4.1 14.6 - - + +
457B PHE 4.0 1.2 + - - -
458B LYS* 1.3 71.7 - - - +
460B HIS* 1.3 68.2 + - - +
461B PHE* 3.8 31.4 - - + -
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Residues in contact with HIS 460 (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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373B ASN* 2.7 31.6 + - + -
374B ILE 2.9 16.5 + - - +
375B GLN* 3.4 29.3 - - + -
376B PHE 2.9 26.6 + - - +
440B ASP* 3.2 13.0 + - - +
441B GLY* 5.2 1.0 + - - -
458B LYS* 3.3 44.2 + - + +
459B LEU* 1.3 75.2 + - - +
461B PHE* 1.3 66.9 + - - +
462B THR* 4.0 1.8 - - + +
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Residues in contact with PHE 461 (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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376B PHE 3.3 12.8 - - - -
378B PRO* 3.6 39.9 - - + -
433B LEU* 3.8 31.4 - - + -
434B LYS* 4.5 5.2 - - + -
438B LEU 3.1 28.5 - - - -
439B VAL* 3.7 1.3 - - - -
440B ASP* 2.7 48.6 + - + +
459B LEU* 3.8 19.3 - - + -
460B HIS* 1.3 74.8 - - - +
462B THR* 1.3 66.3 + - - +
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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