Contacts of the strand formed by residues 391 - 400 (chain B) in PDB entry 1GGT
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 GLY 391 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489A GLU* 5.4 1.4 + - - -
378B ALA 3.4 2.3 - - - +
379B TRP* 3.5 34.8 - - - -
380B MET 2.8 31.0 + - - +
381B THR* 4.7 0.4 - - - +
390B GLY* 1.3 73.7 - - - -
392B TRP* 1.3 62.0 + - - -
393B GLN* 3.0 10.5 + - - +
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Residues in contact with TRP 392 (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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195B LEU* 5.4 0.4 - - + -
200B GLU* 4.7 5.8 + - - -
204B TYR* 3.8 40.6 - + + -
331B PRO* 3.6 19.5 - - + -
332B ALA* 4.2 0.7 - - - -
333B ARG* 3.8 43.9 - - + +
377B GLU* 3.5 48.7 - - + +
378B ALA 3.6 9.0 - - - -
379B TRP* 3.5 40.9 - + + -
390B GLY 4.2 1.7 + - - +
391B GLY* 1.3 69.8 - - - -
393B GLN* 1.3 64.9 + - - +
413B SER* 4.6 0.5 + - - -
414B VAL* 3.2 30.0 + - + +
415B GLN 4.7 0.9 + - - -
480B THR* 6.6 0.4 - - + -
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Residues in contact with GLN 393 (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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377B GLU* 3.1 7.2 - - - -
378B ALA* 2.8 34.4 + - + +
380B MET* 3.7 27.2 + - + -
382B ARG* 3.0 32.3 + - - +
389B PHE 3.2 20.0 + - - -
390B GLY 3.5 0.2 - - - -
391B GLY 3.0 34.2 + - - +
392B TRP* 1.3 78.3 + - - +
394B ALA* 1.3 62.0 + - - +
395B VAL* 3.7 4.1 + - + +
411B PRO* 3.7 19.3 - - + -
412B ALA 3.4 3.8 - - - +
413B SER* 3.2 22.0 + - - -
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Residues in contact with ALA 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B TRP* 4.0 20.6 - - + +
376B ASN 3.5 6.3 - - - -
377B GLU* 4.3 2.9 - - - -
393B GLN* 1.3 70.8 - - - +
395B VAL* 1.3 59.0 + - - +
396B ASP 4.3 0.2 - - - -
409B CYS 3.9 0.7 - - - +
410B GLY* 3.8 3.6 - - - -
411B PRO* 3.4 3.1 - - - +
412B ALA* 2.8 35.9 + - - +
414B VAL* 4.2 8.9 - - + +
417B ILE* 5.3 0.9 - - + -
431B VAL* 4.2 23.6 - - + +
481B TYR* 4.1 9.4 - - + +
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Residues in contact with VAL 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B SER* 4.5 8.1 - - - +
263B SER* 3.4 35.4 - - - +
321B PHE* 3.7 21.3 - - + -
375B TRP* 3.6 1.2 - - - +
376B ASN* 2.8 38.0 + - + +
378B ALA* 4.7 13.5 - - + +
393B GLN 4.1 8.3 - - - +
394B ALA* 1.3 79.0 - - - +
396B ASP* 1.3 63.2 + - - +
397B SER 4.1 0.4 - - - +
408B ARG* 5.1 0.2 - - - -
409B CYS 3.4 9.2 - - - +
410B GLY 4.9 5.2 - - - +
411B PRO* 4.1 22.7 - - + -
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Residues in contact with ASP 396 (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 HIS* 3.4 15.9 + - - -
373B HIS* 3.2 24.8 + - - -
374B CYS 4.0 2.3 - - - +
375B TRP* 3.6 25.2 - - + +
395B VAL* 1.3 74.7 - - - +
397B SER* 1.3 58.1 + - - +
398B THR* 2.9 26.8 + - - +
400B GLN* 4.3 4.0 + - - -
408B ARG* 3.1 7.0 - - - -
409B CYS* 2.9 42.1 + - + +
431B VAL* 6.0 5.4 - - + -
434B GLU* 4.1 3.8 - - - +
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Residues in contact with SER 397 (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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263B SER* 3.9 18.6 + - - +
266B VAL* 4.1 18.8 - - - -
267B ASN* 4.0 10.0 - - - +
317B PHE* 4.2 14.1 + - - +
318B ALA* 4.9 0.2 - - - -
321B PHE* 4.0 25.6 - - - +
375B TRP* 5.7 0.2 - - - +
376B ASN* 4.0 9.6 + - - -
395B VAL* 4.1 1.6 - - - +
396B ASP* 1.3 70.3 + - - +
398B THR* 1.3 60.4 + - - +
399B PRO* 3.0 17.4 - - - +
408B ARG* 3.6 14.6 - - - +
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Residues in contact with THR 398 (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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279B TRP* 4.3 19.3 - - + -
314B CYS* 3.6 10.9 + - + +
317B PHE* 3.5 26.7 - - + +
342B HIS* 3.5 18.2 - - + +
370B TRP* 4.5 4.3 - - + -
373B HIS* 3.4 24.5 - - + -
374B CYS 4.2 1.2 + - - -
396B ASP* 2.9 31.1 + - - +
397B SER* 1.3 74.5 - - - +
399B PRO* 1.3 74.6 - - + +
400B GLN* 3.8 1.4 + - - +
407B TYR 4.4 1.9 - - - +
409B CYS* 5.1 0.9 + - - -
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Residues in contact with PRO 399 (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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267B ASN* 3.6 33.4 - - + +
279B TRP* 5.9 1.1 - - + -
317B PHE* 4.6 2.9 - - + -
342B HIS* 2.9 18.5 + - - -
343B ASP* 4.3 2.1 - - - +
397B SER 3.0 11.0 - - - +
398B THR* 1.3 90.6 - - + +
400B GLN* 1.3 60.1 + - - +
406B MET* 3.9 39.4 - - + +
407B TYR* 3.4 15.5 - - - +
408B ARG 4.6 1.3 - - - +
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Residues in contact with GLN 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B HIS* 3.5 14.6 - - + +
343B ASP* 3.3 33.5 + - - +
344B ASN* 3.4 22.3 + - - +
345B ASP 4.4 3.1 + - - -
396B ASP* 4.3 4.4 + - - -
398B THR 4.9 0.2 - - - +
399B PRO* 1.3 79.5 - - - +
401B GLU* 1.3 69.9 + - - +
402B ASN* 3.3 1.9 + - - -
406B MET* 3.6 9.2 - - - -
407B TYR 3.1 20.0 + - - +
409B CYS* 4.0 20.9 - - - +
430B PHE* 3.9 19.9 + - - +
431B VAL* 5.6 0.6 - - - +
434B GLU* 3.1 24.5 + - - +
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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