Contacts of the strand formed by residues 391 - 400 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378A ALA 3.3 2.6 - - - +
379A TRP* 3.6 36.3 - - - -
380A MET 2.8 33.1 + - - +
390A GLY* 1.3 74.4 - - - -
392A TRP* 1.3 61.9 + - - -
393A GLN* 3.5 3.2 + - - -
489B GLU* 4.8 0.8 + - - -
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Residues in contact with TRP 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A GLU* 5.5 2.9 + - - -
204A TYR* 3.6 44.6 - + + -
331A PRO 3.8 8.1 - - - -
332A ALA* 4.0 1.3 - - - -
333A ARG* 3.5 38.5 - - + +
377A GLU* 3.1 52.0 - - + +
378A ALA 3.5 19.7 - - - -
379A TRP* 3.0 46.2 - + + +
390A GLY 4.2 1.1 + - - +
391A GLY* 1.3 71.5 - - - -
393A GLN* 1.3 64.3 + - - +
413A SER* 4.8 0.2 + - - -
414A VAL* 3.1 30.3 + - + +
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Residues in contact with GLN 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLU* 3.4 4.0 - - - -
378A ALA 3.0 34.6 + - - +
380A MET* 3.9 19.3 + - + -
382A ARG* 2.6 43.4 + - - +
389A PHE 2.9 24.4 + - - -
390A GLY 3.8 4.2 - - - -
391A GLY 3.5 15.7 + - - +
392A TRP* 1.3 78.6 + - - +
394A ALA* 1.3 63.3 + - - +
395A VAL* 3.6 4.4 + - + +
411A PRO* 3.7 21.1 - - + -
412A ALA 3.2 8.5 - - - +
413A SER* 3.2 14.9 - - - -
414A VAL* 4.3 0.9 - - - -
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Residues in contact with ALA 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A TRP* 3.7 26.9 - - + +
376A ASN 3.4 6.3 - - - -
377A GLU* 4.3 1.8 - - - -
393A GLN* 1.3 72.4 - - - +
395A VAL* 1.3 60.0 + - - +
396A ASP* 4.3 0.4 - - + -
409A CYS 4.1 0.6 - - - +
410A GLY* 3.7 2.9 - - - -
411A PRO* 3.4 2.8 - - - +
412A ALA* 2.7 38.1 + - - +
414A VAL* 3.9 7.4 - - + +
417A ILE* 4.9 0.7 - - + -
431A VAL* 4.4 22.3 - - + +
481A TYR* 3.7 11.0 - - + +
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Residues in contact with VAL 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A SER* 4.4 14.8 - - - +
263A SER* 3.4 36.1 - - - +
321A PHE* 3.8 18.8 - - + -
375A TRP* 3.8 1.9 - - - +
376A ASN* 3.0 34.7 + - + +
378A ALA* 5.0 7.9 - - + +
393A GLN 3.9 8.1 - - - +
394A ALA* 1.3 79.0 - - - +
396A ASP* 1.3 63.9 + - - +
397A SER 4.1 0.6 + - - +
408A ARG* 4.5 2.0 - - + -
409A CYS 3.3 9.2 - - - +
410A GLY 4.8 2.9 - - - -
411A PRO* 3.8 23.3 - - + -
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Residues in contact with ASP 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A HIS* 3.6 3.8 - - - -
373A HIS* 2.7 30.5 + - - -
374A CYS 4.1 4.7 - - - +
375A TRP* 3.9 19.2 - - + +
394A ALA* 6.4 0.2 - - + -
395A VAL* 1.3 72.2 - - - +
397A SER* 1.3 59.4 + - - +
398A THR* 3.0 39.1 + - - +
400A GLN* 4.6 1.8 + - - +
408A ARG* 3.0 8.3 - - - +
409A CYS* 2.8 46.9 + - + +
431A VAL* 5.2 7.9 - - + -
434A GLU* 3.6 13.7 - - - +
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Residues in contact with SER 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A SER* 3.4 27.2 - - - +
266A VAL* 3.9 16.2 - - - +
267A ASN* 3.9 13.3 - - - +
317A PHE* 3.6 32.9 + - - +
318A ALA 4.4 0.3 + - - -
321A PHE* 4.4 7.2 - - - +
375A TRP* 5.9 0.4 - - - +
376A ASN* 4.4 6.0 + - - -
395A VAL* 4.0 3.2 + - - +
396A ASP* 1.3 70.9 + - - +
398A THR* 1.3 58.2 + - - +
399A PRO* 3.3 13.3 - - - +
408A ARG* 3.7 11.8 - - - +
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Residues in contact with THR 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A TRP* 4.4 22.7 - - + -
314A CYS* 3.5 13.9 + - + +
317A PHE* 3.6 13.3 - - + +
342A HIS* 3.7 24.9 - - + +
370A TRP* 4.4 7.2 - - + -
373A HIS* 3.3 22.4 - - + -
374A CYS 4.5 1.2 + - - -
396A ASP* 3.0 24.5 + - - +
397A SER* 1.3 74.3 + - - +
399A PRO* 1.3 78.8 - - + +
400A GLN* 3.7 2.3 + - - +
407A TYR 4.3 1.0 - - - +
409A CYS* 5.2 0.7 + - - -
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Residues in contact with PRO 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ASN* 3.1 41.3 - - + +
279A TRP* 6.1 0.7 - - + -
317A PHE* 4.6 2.9 - - + -
342A HIS* 3.1 10.6 + - - -
343A ASP* 4.3 3.1 - - - +
397A SER 3.3 8.0 - - - +
398A THR* 1.3 97.9 - - + +
400A GLN* 1.3 62.4 + - - +
406A MET* 3.8 32.2 - - + +
407A TYR* 3.2 16.6 - - - +
408A ARG 4.9 0.9 - - - +
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Residues in contact with GLN 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A HIS* 3.8 12.4 - - - +
343A ASP* 3.3 35.4 + - - +
344A ASN* 3.7 16.5 + - - +
396A ASP* 4.6 3.2 + - - -
398A THR 4.9 1.0 + - - +
399A PRO* 1.3 79.5 - - - +
401A GLU* 1.3 70.6 + - - +
402A ASN* 3.2 3.6 + - - -
406A MET* 3.2 12.2 - - - -
407A TYR 3.0 23.8 + - - +
409A CYS* 3.5 30.3 - - - +
430A PHE* 3.8 19.1 + - + +
431A VAL* 5.3 1.6 - - - +
434A GLU* 3.1 23.4 + - - +
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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