Contacts of the strand formed by residues 407 - 413 (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 TYR 407 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264B ALA* 5.4 9.2 - - + -
269B LYS* 2.9 31.5 + - + +
398B THR 4.4 0.2 - - - +
399B PRO* 3.4 11.1 - - - +
400B GLN 3.1 22.7 + - - +
402B ASN* 3.7 8.4 + - - +
404B ASP* 3.6 26.2 - - + -
405B GLY 3.3 28.0 - - - -
406B MET* 1.3 78.9 - - - +
408B ARG* 1.3 95.6 + - - +
409B CYS* 3.8 3.3 - - - -
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Residues in contact with ARG 408 (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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260B ARG* 2.9 69.0 + - - +
263B SER* 2.9 26.2 - - - +
264B ALA* 3.8 27.0 - - + +
396B ASP 3.1 18.2 - - - +
397B SER* 3.6 21.3 - - - +
398B THR 4.5 1.1 - - - -
399B PRO* 4.2 3.4 - - - +
402B ASN* 3.4 7.7 + - - +
404B ASP* 5.1 2.6 + - - -
407B TYR* 1.3 100.4 - - + +
409B CYS* 1.3 61.5 + - - +
410B GLY 4.0 5.4 + - - -
427B ASP* 4.4 1.0 + - - -
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Residues in contact with CYS 409 (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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394B ALA 3.9 1.3 - - - +
395B VAL* 3.4 6.2 - - - +
396B ASP* 2.9 39.8 + - + +
398B THR 5.6 1.1 - - - -
400B GLN* 4.0 26.7 - - - +
402B ASN* 3.8 13.7 - - - -
407B TYR 3.8 8.5 - - - -
408B ARG* 1.3 80.2 - - - +
410B GLY* 1.3 62.1 + - - +
427B ASP* 3.4 18.2 - - + -
430B PHE* 4.1 13.2 - - - -
431B VAL* 4.2 17.2 - - + +
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Residues in contact with GLY 410 (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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260B ARG* 2.8 23.9 + - - -
263B SER* 4.9 0.3 + - - -
394B ALA 3.8 2.0 - - - -
395B VAL* 4.9 3.6 - - - -
408B ARG* 4.0 5.5 - - - -
409B CYS* 1.3 75.8 - - - +
411B PRO* 1.3 76.3 - - - +
412B ALA* 3.4 3.4 - - - -
426B PHE* 3.2 17.9 + - - -
427B ASP* 2.8 12.3 + - - -
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Residues in contact with PRO 411 (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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256B ILE* 4.2 11.7 - - + +
259B SER* 3.4 22.9 - - - +
260B ARG* 3.8 16.8 - - + -
380B MET* 4.9 4.3 - - + -
382B ARG* 2.6 33.5 + - - +
393B GLN* 3.7 24.0 - - + -
394B ALA 3.4 8.3 - - - +
395B VAL* 4.1 10.7 - - + -
410B GLY* 1.3 77.9 - - - +
412B ALA* 1.3 55.9 + - - +
425B GLN 2.9 0.2 - - - +
426B PHE* 2.7 33.2 - - + +
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Residues in contact with ALA 412 (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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393B GLN* 3.4 2.2 - - - -
394B ALA* 2.8 34.8 + - - +
410B GLY* 3.4 0.4 - - - -
411B PRO* 1.3 73.5 - - - +
413B SER* 1.3 63.4 + - - +
414B VAL 3.3 0.2 + - - -
417B ILE* 4.0 8.5 - - + -
425B GLN 4.0 3.6 - - - -
426B PHE 3.0 18.6 - - - +
428B ALA* 3.7 23.8 - - + -
431B VAL* 3.8 18.2 - - + -
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Residues in contact with SER 413 (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 ARG* 4.3 2.6 - - - +
385B LEU* 4.5 7.6 - - - -
389B PHE* 3.0 35.4 + - - +
390B GLY 5.2 0.3 + - - -
392B TRP 4.6 0.5 + - - -
393B GLN* 3.2 22.4 + - - -
411B PRO 4.2 0.2 + - - -
412B ALA* 1.3 72.2 - - - +
414B VAL* 1.3 65.3 + - - +
415B GLN* 3.5 5.0 + - - +
416B ALA* 2.9 28.9 + - - +
417B ILE* 2.9 23.2 + - - +
424B PHE 5.7 0.8 + - - -
425B GLN 4.8 0.8 + - - -
428B ALA* 5.5 0.8 - - - +
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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