Contacts of the strand formed by residues 331 - 337 (chain A) in PDB entry 3PE7
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 THR 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A PHE* 3.6 4.4 - - - +
326A ASN* 2.8 32.6 + - - +
329A ASN* 3.3 38.4 + - + +
330A GLY* 1.3 82.1 - - - +
332A GLN* 1.3 61.8 + - - +
333A HIS* 2.8 29.1 + - + -
388A LYS* 3.9 14.4 - - - +
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Residues in contact with GLN 332 (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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281A SER* 4.1 10.2 + - - +
282A MET* 4.1 0.7 - - - -
283A PRO* 3.4 38.2 - - - +
323A TYR* 4.0 17.7 - - + -
324A VAL 3.6 3.8 - - - +
325A PHE* 3.7 22.5 - - + +
330A GLY 4.2 0.4 + - - +
331A THR* 1.3 75.6 - - - +
333A HIS* 1.3 72.3 + - - +
334A ARG 4.4 0.3 + - - -
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Residues in contact with HIS 333 (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 TYR* 3.2 8.5 - - - -
324A VAL 2.8 47.7 + - - +
326A ASN* 4.2 5.6 - - + +
329A ASN* 6.1 0.2 - - - -
331A THR* 2.8 37.5 + - + -
332A GLN* 1.3 81.8 + - - +
334A ARG* 1.3 60.9 + - - +
335A VAL* 3.3 19.8 + - + +
383A PRO* 5.5 1.6 - - + -
385A SER* 3.2 35.2 + - - -
386A VAL* 3.7 27.8 + - + +
388A LYS* 6.0 2.7 - - + -
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Residues in contact with ARG 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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18A SER* 5.4 6.7 + - - -
19A THR* 3.4 18.8 - - + +
321A PHE* 3.5 67.3 - - + -
322A LEU 3.8 3.6 - - - -
323A TYR* 4.0 19.8 + - + -
332A GLN* 4.3 0.8 + - - +
333A HIS* 1.3 70.1 - - - +
335A VAL* 1.3 59.8 + - - +
383A PRO* 5.7 1.0 - - - +
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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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19A THR* 2.7 23.7 + - - -
21A ALA* 3.3 12.5 - - - +
322A LEU* 3.0 16.5 + - + +
324A VAL* 3.9 24.0 - - + -
333A HIS* 3.6 28.9 - - + +
334A ARG* 1.3 75.0 - - - +
336A ALA* 1.3 63.9 + - + +
365A ILE* 3.9 27.8 - - + -
380A ALA* 5.7 1.3 - - + -
381A THR 5.5 0.7 - - - +
382A LEU* 4.3 6.7 - - + -
383A PRO* 3.8 30.8 - - + +
386A VAL* 4.1 2.9 - - + -
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Residues in contact with ALA 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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16A ASP* 3.6 20.4 - - + +
19A THR* 3.8 4.2 - - - +
21A ALA* 4.6 1.1 - - + -
23A VAL* 4.6 5.2 - - + -
321A PHE* 3.5 7.7 - - - -
322A LEU* 2.8 36.3 + - + +
334A ARG 3.7 1.0 - - - -
335A VAL* 1.3 86.4 - - + +
337A ARG* 1.3 62.0 + - - +
367A PHE* 5.6 0.4 - - + -
380A ALA* 4.0 26.7 - - + -
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Residues in contact with ARG 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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16A ASP* 2.7 32.3 + - - +
17A ALA* 4.2 13.1 - - - +
18A SER* 2.9 29.6 + - - +
23A VAL* 5.8 1.2 - - - +
320A PRO* 3.3 26.1 - - - +
321A PHE* 3.6 30.2 - - + +
322A LEU* 4.2 2.0 - - - -
336A ALA* 1.3 74.5 - - - +
338A HIS* 1.3 60.6 + - - +
339A ASP* 2.8 45.4 + - - +
367A PHE* 3.8 14.2 - - - -
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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