Contacts of the strand formed by residues 332 - 340 (chain A) in PDB entry 2D9P
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 SER 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A LEU* 3.9 11.1 + - - +
303A ASP* 3.5 31.9 + - - +
305A ILE 4.9 8.7 - - - -
306A ASP* 6.1 0.2 - - - -
325A VAL* 4.8 7.0 - - - -
326A MET 4.6 0.9 - - - -
327A MET* 3.6 26.4 - - - +
328A GLU* 5.2 0.2 - - - -
331A ARG* 1.3 74.7 - - - +
333A LYS* 1.3 69.7 + - - +
334A GLY* 3.0 5.6 + - - -
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Residues in contact with LYS 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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326A MET* 3.2 24.4 + - + +
327A MET 4.4 1.8 + - - -
328A GLU* 3.9 37.0 - - + +
331A ARG 3.7 4.6 + - - -
332A SER* 1.3 70.3 - - - +
334A GLY* 1.3 58.8 + - - +
335A PHE* 3.4 37.9 - - + -
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Residues in contact with GLY 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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299A LYS* 3.6 2.3 - - - +
300A ASN* 2.9 25.9 + - - -
301A LEU* 3.8 26.0 - - - -
325A VAL* 5.4 0.4 - - - +
326A MET 4.3 1.0 + - - -
332A SER* 3.0 7.6 + - - -
333A LYS* 1.3 78.7 - - - +
335A PHE* 1.3 71.1 + - - +
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Residues in contact with PHE 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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297A TYR* 4.1 24.0 - + + +
298A VAL 3.1 16.6 - - - +
299A LYS* 4.0 5.2 - - + +
301A LEU* 3.6 13.1 - - - +
325A VAL* 3.7 1.6 - - - +
326A MET* 3.1 45.0 + - + +
333A LYS* 3.4 40.2 - - + -
334A GLY* 1.3 87.1 - - - +
336A GLY* 1.3 58.3 + - - +
337A PHE* 5.2 8.3 - + - -
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Residues in contact with GLY 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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297A TYR* 4.3 1.4 - - - -
298A VAL* 2.8 33.4 + - - +
301A LEU* 3.6 8.6 - - - +
310A LEU* 4.8 1.3 - - - -
324A LYS 3.5 11.9 - - - -
325A VAL* 3.9 7.6 - - - -
326A MET* 4.2 2.7 - - - -
335A PHE* 1.3 74.5 - - - +
337A PHE* 1.3 77.2 + - - -
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Residues in contact with PHE 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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295A ASN* 6.4 2.7 - - + -
296A LEU 3.5 13.9 - - - +
297A TYR* 3.7 31.9 - + + -
310A LEU* 4.8 0.2 - - - +
322A SER 3.9 1.7 - - - +
323A ALA* 3.4 2.1 - - - -
324A LYS* 3.0 43.9 + - + +
326A MET* 4.5 30.7 - - + -
335A PHE* 5.2 7.0 - + - -
336A GLY* 1.3 80.6 - - - -
338A VAL* 1.3 66.0 + - - +
339A CYS* 5.8 4.0 - - - -
368A ALA* 5.3 8.5 - - + -
371A LYS* 6.6 0.4 - - + -
372A GLU* 5.0 23.6 - - + -
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Residues in contact with VAL 338 (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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294A VAL 3.6 1.2 - - - +
295A ASN* 3.6 0.5 - - - -
296A LEU* 2.7 43.7 + - + +
298A VAL* 3.9 5.8 - - + -
310A LEU* 3.6 28.7 - - + -
311A ARG* 5.5 0.4 - - - -
314A PHE* 3.3 46.7 - - + -
320A ILE* 4.0 18.4 - - + -
322A SER 3.4 3.4 - - - -
323A ALA* 4.2 7.2 - - + +
337A PHE* 1.3 82.1 - - - +
339A CYS* 1.3 64.3 + - - +
340A PHE* 3.8 11.2 - - + -
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Residues in contact with CYS 339 (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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294A VAL* 4.0 9.4 - - + -
295A ASN* 4.0 22.4 - - - -
320A ILE* 3.0 29.6 - - - +
321A THR* 3.4 8.0 + - - +
322A SER* 2.6 39.2 + - - +
337A PHE* 5.8 3.4 - - - -
338A VAL* 1.3 79.7 - - - +
340A PHE* 1.3 66.6 + - - +
371A LYS* 6.1 4.3 - - - -
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Residues in contact with PHE 340 (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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294A VAL* 3.6 22.7 + - + +
296A LEU* 3.2 34.8 - - + -
314A PHE* 3.5 38.4 - + + -
317A PHE* 4.2 3.6 - - + -
318A GLY* 3.4 39.0 - - - -
319A THR 3.2 19.3 - - - -
320A ILE* 4.2 2.0 - - + -
321A THR* 4.4 10.6 + - - +
338A VAL* 3.8 7.2 - - + -
339A CYS* 1.3 78.8 - - - +
341A SER* 1.3 64.2 + - - +
342A SER 3.9 8.1 - - - +
345A GLU* 4.3 10.8 - - + -
346A ALA* 3.7 21.5 - - + -
349A ALA* 3.9 11.0 - - + -
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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