Contacts of the strand formed by residues 406 - 417 (chain A) in PDB entry 3IH9
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 406 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A ASP* 3.9 4.3 + - - -
326A ARG* 3.4 28.4 + - - +
327A VAL 3.0 24.4 + - - -
404A ILE* 3.7 3.9 - - - +
405A ARG* 1.3 88.8 + - - +
407A VAL* 1.3 71.4 + - - +
408A VAL* 4.3 3.4 - - + -
438A ARG* 3.2 29.4 + - - +
440A GLU* 3.8 31.0 - - + +
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Residues in contact with VAL 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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327A VAL* 3.4 12.1 - - + +
329A LEU* 4.9 10.1 - - + -
347A LEU* 4.7 10.1 - - + -
350A LEU* 4.4 15.3 - - + -
404A ILE* 4.0 13.0 - - + -
406A THR* 1.3 80.2 - - - +
408A VAL* 1.3 70.3 + - - +
409A LEU* 5.0 4.0 - - + +
432A LEU* 4.1 28.3 - - + -
437A VAL* 3.5 20.0 - - + -
438A ARG 2.7 10.8 + - - +
439A VAL* 3.2 10.3 - - + +
440A GLU 3.0 23.0 + - - -
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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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326A ARG* 4.2 19.7 - - + +
327A VAL 2.9 15.1 + - - +
328A PHE* 3.9 22.8 - - + +
329A LEU* 2.9 31.5 + - - +
330A HIS* 5.3 0.8 + - + -
406A THR* 4.4 3.1 - - + -
407A VAL* 1.3 74.3 - - - +
409A LEU* 1.3 65.8 + - - +
410A ASN* 3.7 2.9 + - + +
440A GLU* 3.2 30.5 - - + +
442A GLU* 3.4 42.2 - - + +
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Residues in contact with LEU 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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329A LEU* 3.7 30.7 - - + +
331A LEU* 4.0 25.6 - - + -
343A VAL* 5.4 4.0 - - + -
347A LEU* 5.5 7.9 - - + -
407A VAL* 3.9 7.0 + - + -
408A VAL* 1.3 71.5 - - - +
410A ASN* 1.3 57.1 + - - +
411A LEU* 3.8 6.9 + - + -
425A ILE* 4.4 15.9 - - + -
429A VAL* 3.6 31.9 - - + -
432A LEU* 6.3 1.3 - - + -
439A VAL* 5.2 6.5 - - + -
440A GLU 2.7 12.5 + - - +
441A VAL* 3.3 20.0 - - + +
442A GLU 2.7 32.9 + - - +
448A LEU* 5.7 1.8 - - + -
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Residues in contact with ASN 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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329A LEU 3.1 7.7 + - - +
330A HIS* 3.3 43.9 + - + +
331A LEU* 3.1 26.7 + - - +
408A VAL* 3.7 2.1 + - + +
409A LEU* 1.3 73.4 - - - +
411A LEU* 1.3 62.4 + - - +
412A ALA* 2.8 40.9 + - - +
413A ARG* 4.2 2.6 + - - +
442A GLU* 3.2 32.8 + - - +
444A PRO* 5.7 0.6 - - - +
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Residues in contact with LEU 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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331A LEU* 3.8 26.7 - - + -
409A LEU* 4.1 18.4 - - + +
410A ASN* 1.3 81.3 - - - +
412A ALA* 1.3 66.6 + - - +
413A ARG 3.1 3.1 - - - -
414A VAL* 2.8 35.2 + - + +
425A ILE* 6.0 1.6 - - + -
441A VAL* 3.7 18.4 - - + -
442A GLU 3.0 13.5 + - - +
443A ASP* 3.3 29.6 - - - +
444A PRO* 4.7 1.8 - - - -
447A ILE* 4.8 10.9 - - + +
448A LEU* 3.9 19.5 - - + +
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Residues in contact with ALA 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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410A ASN* 2.8 23.5 + - - +
411A LEU* 1.3 77.1 - - - +
413A ARG* 1.3 62.4 + - + +
414A VAL 3.5 4.2 + - - +
444A PRO* 3.8 31.4 - - + +
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Residues in contact with ARG 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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318A ARG* 3.5 48.8 - - - +
330A HIS* 5.9 4.9 - - + -
331A LEU 3.4 16.2 + - - +
332A GLN* 3.5 21.2 - - + +
333A GLY 3.6 4.2 + - - -
410A ASN* 4.2 2.1 + - - +
411A LEU 3.1 1.2 - - - -
412A ALA* 1.3 79.9 - - + +
414A VAL* 1.3 61.1 + - - +
415A ASP* 3.6 8.7 + - - +
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Residues in contact with VAL 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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331A LEU* 3.2 43.1 - - + +
332A GLN* 3.3 4.9 - - - +
333A GLY 3.4 14.4 - - - +
335A ILE* 3.8 16.6 - - + -
411A LEU* 2.8 28.5 + - + +
412A ALA 4.1 4.3 - - - +
413A ARG* 1.3 78.6 - - - +
415A ASP* 1.3 63.9 + - - +
416A ARG* 3.8 15.7 - - - +
417A ILE* 4.9 4.5 - - + +
447A ILE* 3.4 22.9 - - + +
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Residues in contact with ASP 415 (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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333A GLY* 3.1 28.6 + - - +
334A VAL* 4.3 9.0 + - + +
413A ARG 4.5 5.4 - - - +
414A VAL* 1.3 74.4 - - - +
416A ARG* 1.3 71.5 + - + +
447A ILE* 3.8 10.0 - - - +
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Residues in contact with ARG 416 (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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213A THR* 4.7 12.1 + - - -
216A ILE* 3.1 38.4 - - - +
223A ARG* 4.5 6.7 - - - +
333A GLY 3.7 1.4 - - - +
334A VAL* 3.5 36.8 - - + +
335A ILE 3.1 22.9 + - - -
414A VAL* 3.5 8.0 - - - +
415A ASP* 1.3 83.7 - - + +
417A ILE* 1.3 64.8 + - - +
447A ILE* 4.4 8.7 - - - -
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Residues in contact with ILE 417 (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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334A VAL* 5.8 0.4 - - - -
335A ILE* 3.1 28.5 - - + +
414A VAL* 4.9 2.7 - - + -
416A ARG* 1.3 81.5 - - - +
418A ASP* 1.3 65.3 + - - +
421A GLY 3.3 28.7 - - - +
422A ARG* 2.9 38.3 + - + +
425A ILE* 3.5 24.7 - - + -
447A ILE* 3.6 27.6 - - + +
448A LEU* 5.0 5.2 - - + +
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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