Contacts of the strand formed by residues 406 - 414 (chain A) in PDB entry 3H4B
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 LEU 406 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A GLU* 5.0 0.4 - - - -
306A ASP* 2.9 32.0 + - + +
308A PHE* 3.9 24.2 - - + -
312A SER* 4.5 8.1 - - - +
317A ALA 3.8 21.5 - - - +
320A LYS* 4.6 5.8 - - + -
321A ILE* 4.0 26.5 - - + -
324A LEU* 3.5 16.6 - - + +
345A ILE 3.7 2.7 - - - +
346A ILE* 3.4 27.8 - - + -
391A PHE* 5.9 9.0 - - + -
404A THR 6.2 0.4 - - - +
405A LEU* 1.3 86.2 - - - +
407A SER* 1.3 61.7 + - - +
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Residues in contact with SER 407 (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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303A SER* 5.6 2.2 - - - -
304A GLU 2.9 21.1 - - - -
305A GLU* 3.5 22.4 + - - +
324A LEU* 3.6 2.7 - - - +
343A ARG 3.9 0.2 - - - +
344A LEU* 3.5 5.4 - - - +
345A ILE* 3.1 55.1 + - - +
406A LEU* 1.3 76.0 - - - +
408A VAL* 1.3 65.3 + - - +
409A CYS* 6.0 0.2 - - - +
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Residues in contact with VAL 408 (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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303A SER* 3.2 19.4 - - - -
304A GLU 3.3 13.2 + - - +
321A ILE* 4.1 7.4 - - + -
324A LEU* 3.7 16.0 - - + +
325A LEU* 3.3 27.4 - - + -
328A LEU* 3.4 24.4 - - + +
342A VAL* 4.1 5.2 - - + -
343A ARG 3.4 11.4 - - - +
344A LEU* 4.8 4.0 - - + -
387A LEU* 3.7 16.8 - - + -
407A SER* 1.3 78.8 - - - +
409A CYS* 1.3 65.5 + - - +
410A PHE* 3.6 18.4 - - + -
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Residues in contact with CYS 409 (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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301A SER* 4.2 17.0 - - - -
302A PHE 3.4 11.0 - - - -
303A SER* 3.8 12.3 - - - -
342A VAL* 3.4 5.7 - - - -
343A ARG* 3.1 50.6 + - + +
345A ILE* 5.3 8.3 - - + -
408A VAL* 1.3 79.2 - - - +
410A PHE* 1.3 73.0 + - - +
411A CYS* 3.6 11.9 + - - -
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Residues in contact with PHE 410 (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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301A SER* 3.6 2.4 - - - -
302A PHE* 2.8 34.4 + - + +
325A LEU* 4.9 4.9 - - + -
328A LEU* 3.7 30.1 - - + -
329A LEU* 3.7 26.2 - - + -
332A VAL* 3.6 26.9 - - + -
339A PRO* 3.4 30.5 - - + -
341A THR 3.6 3.8 - - - -
342A VAL* 4.1 10.8 - - + -
364A ILE* 4.2 17.0 - - + -
383A MET* 4.6 13.9 - - + -
408A VAL* 3.6 21.8 - - + -
409A CYS* 1.3 76.1 - - - +
411A CYS* 1.3 58.9 + - - +
413A LEU* 3.8 4.5 - - - +
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Residues in contact with CYS 411 (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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300A GLN 4.3 2.7 - - - +
301A SER* 4.3 9.2 - - - -
339A PRO* 3.6 2.8 - - - +
340A HIS 3.6 2.4 + - - -
341A THR* 3.2 45.2 + - - +
343A ARG* 3.9 27.1 - - - +
361A GLN* 5.1 1.8 - - - -
409A CYS* 4.2 16.8 - - - -
410A PHE* 1.3 75.6 - - - +
412A ASN* 1.3 77.8 + - - +
413A LEU* 3.5 7.2 - - - -
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Residues in contact with ASN 412 (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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300A GLN 4.2 4.2 + - - -
340A HIS* 2.8 30.7 + - - +
341A THR* 3.4 24.4 + - - +
411A CYS* 1.3 80.2 - - - +
413A LEU* 1.3 62.0 + - - +
414A LYS* 3.1 29.2 + - - +
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Residues in contact with LEU 413 (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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300A GLN* 3.5 27.3 + - - +
302A PHE* 3.6 24.0 - - + -
332A VAL* 5.0 2.2 - - + -
335A ASP* 4.6 1.3 - - - +
337A ARG* 3.2 42.6 - - + +
338A LYS 3.8 5.4 - - - +
339A PRO* 3.7 28.0 - - + -
410A PHE 3.8 7.9 - - - +
411A CYS* 3.5 20.4 - - - -
412A ASN* 1.3 69.9 - - - +
414A LYS* 1.3 72.8 - - - +
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Residues in contact with LYS 414 (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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337A ARG* 3.1 20.2 - - - +
338A LYS* 3.0 31.6 + - - +
340A HIS* 3.4 38.3 + - + +
412A ASN* 3.1 29.3 + - - +
413A LEU* 1.3 87.1 - - - +
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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