Contacts of the strand formed by residues 333 - 337 (chain A) in PDB entry 4GGA
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 VAL 333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A ALA* 5.2 0.9 - - + -
326A SER 3.3 10.1 - - - +
332A LEU* 1.3 80.4 - - - +
334A ASN* 1.3 72.0 + - - +
335A VAL* 4.6 0.2 - - + -
350A THR* 3.3 4.7 - - - +
351A PHE* 2.8 62.1 + - + +
354A HIS* 4.0 19.7 - - + -
358A VAL* 3.8 25.8 - - + -
361A VAL* 6.0 0.7 - - + -
371A LEU* 4.2 10.8 - - + -
373A THR* 4.0 20.9 - - + +
385A TRP* 5.1 0.2 - - - +
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Residues in contact with ASN 334 (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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307A GLY* 3.0 35.2 + - - -
308A HIS* 3.3 19.8 + - - -
324A LEU 3.8 0.3 - - - +
325A ALA* 3.3 4.3 - - - +
326A SER* 2.9 43.0 + - - +
332A LEU* 4.2 2.5 - - - +
333A VAL* 1.3 75.5 - - - +
335A VAL* 1.3 64.1 + - - +
336A TRP* 3.5 13.3 - - + +
347A PRO* 3.6 12.9 - - + +
349A GLN 3.4 2.2 - - - +
350A THR* 2.9 36.9 + - - +
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Residues in contact with VAL 335 (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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323A HIS* 3.9 36.1 - - + -
324A LEU 3.4 4.3 - - - +
325A ALA* 4.8 1.6 - - + -
333A VAL* 4.6 0.7 - - + -
334A ASN* 1.3 78.9 - - - +
336A TRP* 1.3 55.9 - - - +
347A PRO* 3.5 2.8 - - - +
348A LEU* 2.7 34.8 + - + +
349A GLN* 2.8 27.0 + - + +
351A PHE* 4.1 26.5 - - + -
363A TRP* 4.1 8.3 - - + -
371A LEU* 4.1 19.5 - - + -
387A VAL* 4.2 12.6 - - + -
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Residues in contact with TRP 336 (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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290A ILE* 3.7 14.6 - - + +
305A LEU* 3.6 34.8 - - + -
306A SER 3.7 10.3 - - - -
307A GLY* 3.6 37.9 - - - -
308A HIS* 4.9 0.2 - + - -
323A HIS* 3.3 11.1 - - - +
324A LEU* 2.7 60.9 + - + +
326A SER* 3.0 24.8 + - - -
334A ASN* 3.5 19.4 - - + +
335A VAL* 1.3 73.1 - - - +
337A PRO* 1.3 74.8 - - + +
345A TRP* 3.7 17.3 - + - -
346A VAL 3.9 7.2 - - - -
347A PRO* 3.6 35.2 - - + -
348A LEU* 4.3 3.4 - - - -
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Residues in contact with PRO 337 (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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292A HIS* 5.4 0.3 + - - -
317A TRP* 4.8 4.4 - - - -
322A ARG 4.4 3.4 - - - +
323A HIS* 5.0 0.4 - - - -
324A LEU* 5.4 0.2 - - - +
336A TRP* 1.3 95.3 - - + +
338A SER* 1.3 60.2 + - - +
339A ALA 3.4 23.1 - - - +
340A PRO* 4.8 2.5 - - + -
341A GLY* 5.1 3.6 - - - +
345A TRP* 3.3 22.4 - - + -
346A VAL 3.4 26.9 - - - +
348A LEU* 3.8 33.4 - - + +
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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