Contacts of the strand formed by residues 412 - 419 (chain A) in PDB entry 3HG2
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 412 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A ASN* 5.2 0.2 + - - -
281A VAL* 3.5 20.6 - - - +
282A THR* 2.8 42.7 + - - +
285A ALA* 3.8 13.0 - - + -
286A LEU* 3.8 19.9 - - + +
352A ALA* 3.8 11.0 - - + -
353A MET 3.2 12.1 - - - +
354A ILE* 3.6 8.3 - - - +
388A LEU* 3.9 1.3 - - - +
389A PRO* 3.7 12.3 - - - +
407A ILE* 4.2 1.6 - - - -
411A GLY* 1.3 74.5 + - - -
413A VAL* 1.3 76.9 + - - +
414A LEU 4.0 0.2 + - - -
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Residues in contact with VAL 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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351A VAL 3.6 1.6 - - - +
352A ALA* 3.3 3.8 - - - -
353A MET* 2.8 66.4 + - + +
386A GLN* 3.8 18.6 - - - +
388A LEU 3.4 4.0 - - - +
389A PRO* 4.0 14.4 - - + -
405A SER* 3.8 12.1 - - - +
406A HIS 4.0 10.1 - - - +
407A ILE* 3.8 22.9 - - + +
412A THR* 1.3 77.0 - - - +
414A LEU* 1.3 60.3 + - - +
415A LEU* 3.8 16.2 - - + -
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Residues in contact with LEU 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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285A ALA* 4.1 18.4 - - + +
288A ALA* 5.2 1.6 - - + -
289A ILE* 3.9 27.1 - - + +
316A VAL* 3.8 35.7 - - + -
319A ILE* 4.0 20.0 - - + -
350A ALA* 4.5 4.5 - - + -
351A VAL 3.3 16.6 - - - +
352A ALA* 4.1 6.5 - - + -
386A GLN* 3.6 3.5 - - - +
387A LEU* 2.7 36.9 + - + -
388A LEU* 3.0 30.6 + - + +
412A THR 4.0 0.4 - - - -
413A VAL* 1.3 73.2 - - - +
415A LEU* 1.3 62.0 + - - +
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Residues in contact with LEU 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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319A ILE* 5.1 0.2 - - - +
350A ALA* 3.3 6.4 - - - +
351A VAL* 2.7 50.1 + - + +
353A MET* 3.7 16.2 - - + -
384A ILE* 4.0 11.9 - - + -
385A THR 3.3 6.1 - - - +
386A GLN* 3.7 19.7 - - + +
387A LEU* 4.5 2.7 - - - +
394A LEU* 3.7 29.2 - - + -
403A LEU* 3.3 35.0 - - + -
405A SER* 5.8 0.4 - - - +
413A VAL* 3.8 16.6 - - + -
414A LEU* 1.3 78.0 - - - +
416A GLN* 1.3 60.6 + - - +
417A LEU* 4.0 6.5 + - + -
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Residues in contact with GLN 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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315A ASP* 4.7 2.9 - - - +
319A ILE* 3.7 22.6 - - + +
344A LEU* 4.0 19.9 - - + +
348A ALA* 4.3 1.8 - - - +
349A TRP 3.4 8.5 - - - +
350A ALA* 4.6 0.2 - - - +
383A PHE 3.6 1.9 - - - +
384A ILE* 3.5 3.5 - - - -
385A THR* 2.8 43.6 + - - +
387A LEU* 4.0 17.0 - - + +
415A LEU* 1.3 73.5 - - - +
417A LEU* 1.3 65.1 + - - +
418A GLU* 2.8 31.6 + - + +
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Residues in contact with LEU 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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347A LEU 4.5 0.2 - - - +
348A ALA* 3.2 10.0 - - - +
349A TRP* 2.8 38.2 + - + +
351A VAL* 3.8 33.2 - - + -
372A LEU* 4.1 17.9 - - + -
377A ALA* 3.8 19.3 - - + -
378A CYS* 3.8 21.1 - - - -
382A CYS* 4.6 5.2 - - + -
383A PHE 3.5 4.0 - - - +
384A ILE* 4.0 25.6 - - + -
415A LEU* 4.0 17.7 - - + -
416A GLN* 1.3 79.2 - - - +
418A GLU* 1.3 62.5 + - - +
419A ASN 4.1 0.4 + - - -
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Residues in contact with GLU 418 (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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346A GLY 4.6 6.2 - - - +
348A ALA* 3.4 19.2 - - - +
382A CYS* 3.1 4.8 - - - -
383A PHE* 2.8 52.1 + - + +
385A THR* 6.0 1.8 - - - +
416A GLN* 2.8 35.9 + - + +
417A LEU* 1.3 73.0 - - - +
419A ASN* 1.3 68.0 + - - +
420A THR* 3.5 0.9 + - - +
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Residues in contact with ASN 419 (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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346A GLY 5.7 0.6 + - - -
347A LEU* 4.0 35.1 + - + +
376A VAL 2.9 28.0 + - - +
377A ALA 3.0 19.4 + - - +
379A ASN 2.9 21.2 + - - +
380A PRO* 4.5 1.6 - - - +
381A ALA 3.7 5.4 + - - +
417A LEU 4.1 1.4 - - - -
418A GLU* 1.3 76.1 + - - +
420A THR* 1.3 62.2 + - - +
421A MET* 3.0 44.3 + - - +
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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