Contacts of the strand formed by residues 322 - 330 (chain A) in PDB entry 1G88
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 322 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A PRO* 3.0 16.1 - - - +
321A GLU* 1.3 115.3 + - + +
323A TRP* 1.3 59.3 + - - +
324A CYS 3.7 11.4 - - - +
340A LYS* 3.7 44.3 + - + +
341A VAL 2.9 14.8 - - - +
342A PRO* 3.5 35.2 - - + -
343A SER* 3.8 3.8 - - - -
530A HIS* 3.0 32.3 + + + +
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Residues in contact with TRP 323 (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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320A PRO* 4.5 6.1 - - + -
322A TYR* 1.3 71.8 - - - +
324A CYS* 1.3 84.5 + - + +
341A VAL* 3.0 18.6 + - + +
342A PRO 3.2 24.2 - - - -
343A SER* 3.8 16.2 + - - +
345A CYS 2.8 23.0 + - - -
346A PRO* 3.8 13.2 - - + +
348A VAL* 4.2 10.3 - - + -
389A LEU* 3.6 42.0 - - + -
390A GLU 4.0 0.4 - - - -
391A CYS* 3.4 42.4 - - + -
397A VAL* 3.8 25.8 - - + -
527A ILE* 5.7 1.1 - - + -
529A LEU* 3.8 5.9 - - + +
530A HIS* 3.0 21.7 + - - +
531A ARG* 4.2 6.7 + - + +
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Residues in contact with CYS 324 (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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322A TYR* 3.2 6.6 - - - +
323A TRP* 1.3 112.1 - - + +
325A SER* 1.3 64.4 + - - +
326A ILE* 3.6 13.0 - - - -
341A VAL* 3.0 49.5 + - - +
348A VAL* 5.0 1.6 - - - -
389A LEU* 5.6 0.4 - - - -
527A ILE* 4.2 15.0 - - + -
528A HIS 3.0 17.3 - - - +
529A LEU* 4.2 2.7 - - + -
530A HIS* 4.0 7.2 - - - -
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Residues in contact with SER 325 (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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324A CYS* 1.3 78.6 - - - +
326A ILE* 1.3 64.8 + - - +
327A ALA* 5.5 0.3 - - - +
338A THR* 4.1 15.3 - - - +
339A PHE 3.1 12.3 - - - -
340A LYS* 4.2 12.8 - - - -
526A GLU 3.7 2.3 - - - +
527A ILE* 3.7 0.5 - - - -
528A HIS* 3.0 36.7 + - - +
530A HIS* 3.3 19.9 + - - -
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Residues in contact with ILE 326 (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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324A CYS* 3.6 11.7 - - - -
325A SER* 1.3 75.0 - - - +
327A ALA* 1.3 64.0 + - - +
328A TYR 4.1 0.4 + - - -
338A THR* 3.3 4.4 - - - +
339A PHE* 2.7 47.8 + - + +
341A VAL* 3.5 31.6 - - + -
348A VAL* 4.6 10.5 - - + -
350A VAL* 4.8 5.2 - - + -
362A PHE* 3.9 24.6 - - + -
389A LEU* 4.4 10.3 - - + -
525A ILE* 3.5 36.3 - - + -
526A GLU 3.6 5.2 - - - +
527A ILE* 4.2 16.4 - - + -
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Residues in contact with ALA 327 (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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326A ILE* 1.3 77.1 - - - +
328A TYR* 1.3 60.2 + - - +
329A PHE* 3.0 26.2 - - + -
334A GLN* 4.0 19.1 - - - +
338A THR* 4.4 11.2 - - + +
525A ILE* 3.3 0.3 - - - -
526A GLU* 2.9 38.9 + - + +
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Residues in contact with TYR 328 (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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326A ILE 4.1 1.2 + - - -
327A ALA* 1.3 72.0 - - - +
329A PHE* 1.3 68.3 + - - +
330A GLU* 2.6 46.0 + - + +
334A GLN* 3.3 7.6 + - - +
335A VAL* 2.8 53.8 + - + +
337A GLU 5.4 0.6 + - - -
362A PHE* 4.0 23.3 - - + -
364A LEU* 3.6 22.9 - - + -
367A LEU* 3.7 16.8 - - + -
372A ARG* 5.0 0.2 - - - -
380A ARG* 2.7 21.0 + - - +
383A ILE* 5.0 2.2 - - + -
505A PHE* 5.4 1.3 - + - -
523A CYS* 3.5 24.1 - - + +
524A TRP 3.3 17.0 - - - -
525A ILE* 3.7 14.1 - - + -
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Residues in contact with PHE 329 (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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327A ALA* 3.0 38.8 - - + -
328A TYR* 1.3 78.7 - - - +
330A GLU* 1.3 64.3 + - - +
331A MET 4.0 2.2 - - - +
332A ASP 4.7 3.6 - - - -
333A VAL* 3.1 11.0 - - - +
334A GLN* 3.6 35.9 - - + -
335A VAL 4.3 0.4 - - - +
523A CYS* 3.4 3.8 - - - -
524A TRP* 2.8 79.9 + + + +
526A GLU* 3.9 23.6 - - + -
368C SER* 6.0 1.8 - - - -
370C VAL* 4.8 11.9 - - + -
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Residues in contact with GLU 330 (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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328A TYR* 2.6 33.1 + - + +
329A PHE* 1.3 70.9 - - - +
331A MET* 1.3 72.7 - - - +
332A ASP 3.0 2.8 + - - -
333A VAL* 2.9 20.5 + - - +
335A VAL* 3.5 21.3 - - + -
369A ASN* 2.8 31.9 + - - +
372A ARG* 3.0 41.8 + - - +
376A ILE* 3.7 14.3 - - + +
380A ARG* 3.1 8.0 + - - -
522A PRO 3.2 11.7 - - - +
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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