Contacts of the strand formed by residues 321 - 326 (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 PHE 321 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A SER* 3.6 28.9 - - - -
19A THR* 4.9 1.6 - - + -
301A GLY* 2.7 33.4 + - - -
319A ASP* 3.2 22.7 + - - +
320A PRO* 1.3 96.6 - - + +
322A LEU* 1.3 57.2 + - - +
323A TYR* 3.8 12.5 - - + -
334A ARG* 3.5 60.3 - - + -
336A ALA 3.5 12.3 - - - -
337A ARG* 3.6 28.3 - - + -
338A HIS* 3.4 3.8 + - - -
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Residues in contact with LEU 322 (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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298A VAL* 4.9 0.9 - - + -
299A GLY 3.5 3.4 - - - +
300A ASP* 3.9 25.8 - - + -
321A PHE* 1.3 72.6 - - - +
323A TYR* 1.3 60.5 + - - +
334A ARG* 3.8 3.6 - - - -
335A VAL* 3.0 28.9 + - + +
336A ALA* 2.8 17.6 + - + +
337A ARG 4.2 2.7 - - - -
338A HIS* 3.9 25.1 - - + +
354A PRO* 4.4 4.3 - - + -
356A PRO* 4.0 24.9 - - + -
365A ILE* 3.9 20.9 - - + -
367A PHE* 3.6 42.0 - - + -
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Residues in contact with TYR 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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283A PRO* 3.7 33.1 - - + +
285A CYS* 3.9 14.1 - - - -
298A VAL* 3.2 7.2 - - - +
299A GLY 3.0 32.1 + - - +
301A GLY* 4.2 3.8 - - - -
319A ASP* 2.7 41.4 + - - -
321A PHE* 3.8 21.4 - - + +
322A LEU* 1.3 75.0 - - - +
324A VAL* 1.3 63.9 + - - +
325A PHE* 3.8 21.6 - - + -
332A GLN* 4.0 16.4 - - + -
333A HIS 3.2 6.1 - - - +
334A ARG* 4.0 35.3 + - + -
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Residues in contact with VAL 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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296A LEU* 4.2 8.5 - - + -
297A MET 3.2 11.2 - - - +
298A VAL* 4.1 12.1 - - + -
323A TYR* 1.3 78.0 - - - +
325A PHE* 1.3 70.4 + - - +
326A ASN 4.7 0.2 - - - +
332A GLN* 3.6 1.6 - - - -
333A HIS* 2.8 42.6 + - + -
335A VAL* 3.9 20.4 - - + -
358A PHE* 4.3 12.1 - - + -
365A ILE* 4.6 0.2 - - + -
382A LEU* 3.8 28.5 - - + -
386A VAL* 4.1 25.8 - - + -
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Residues in contact with PHE 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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266A ILE* 4.2 11.4 - - + -
280A THR* 4.8 5.6 - - + -
281A SER 4.4 4.7 - - - -
282A MET* 3.7 34.1 - - + -
283A PRO* 3.8 6.5 - - + -
285A CYS* 4.8 1.3 - - - -
288A LEU* 4.2 11.2 - - + -
296A LEU* 3.3 7.1 - - - +
297A MET* 2.8 53.6 + - + +
299A GLY* 4.0 12.3 - - - -
323A TYR* 3.8 26.7 - - + -
324A VAL* 1.3 73.8 - - - +
326A ASN* 1.3 62.1 + - - +
327A MET* 3.5 20.4 + - - +
331A THR 3.6 4.9 - - - +
332A GLN* 3.7 38.4 - - + -
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Residues in contact with ASN 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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295A SER 3.9 4.0 - - - +
296A LEU* 4.0 16.8 - - + +
324A VAL 4.0 2.0 + - - -
325A PHE* 1.3 69.2 - - - +
327A MET* 1.3 58.7 + - - +
328A LYS* 3.0 23.2 + - - +
329A ASN* 3.1 25.6 + - - -
330A GLY* 2.8 27.4 + - - -
331A THR* 2.8 30.0 + - - +
333A HIS* 4.2 4.6 - - + +
386A VAL* 2.8 28.3 + - + +
387A TRP* 4.2 12.1 - - - +
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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