Contacts of the strand formed by residues 410 - 422 (chain A) in PDB entry 3HIG
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 VAL 410 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401A PHE* 3.2 9.1 - - - -
402A HIS 2.9 36.8 + - - +
406A ALA* 3.9 17.9 - - + -
408A ASP 3.4 14.8 - - - +
409A PRO* 1.3 72.8 - - - +
411A HIS* 1.3 62.2 + - - +
412A TYR* 3.4 26.5 - - + +
748A TYR* 3.4 16.8 - - + +
749A ARG* 3.4 24.0 - - - +
750A PRO* 4.5 10.3 - - + -
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Residues in contact with HIS 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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399A ASP* 2.8 39.3 + - + +
400A THR 3.7 6.5 - - - -
401A PHE* 3.6 38.2 - + + -
410A VAL* 1.3 71.9 - - - +
412A TYR* 1.3 60.8 + - - +
413A PRO* 3.6 24.3 - - + +
748A TYR* 3.1 28.4 - - - +
749A ARG 2.9 21.6 + - - +
751A VAL* 3.8 14.5 - - + +
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Residues in contact with TYR 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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380A SER* 3.3 25.8 + - - -
382A THR* 3.6 29.4 - - - +
383A HIS* 3.5 29.1 + + - -
399A ASP* 3.4 2.4 - - - +
400A THR* 2.8 38.3 + - + +
402A HIS* 3.6 24.5 - + + +
410A VAL* 3.4 38.1 - - + +
411A HIS* 1.3 75.4 - - - +
413A PRO* 1.3 69.7 - - + +
415A ALA* 4.0 9.6 + - + -
748A TYR* 3.8 19.3 - + + -
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Residues in contact with PRO 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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383A HIS 4.7 0.3 - - - -
384A GLU* 3.5 39.0 + - + +
399A ASP* 3.4 12.1 - - - +
411A HIS* 3.6 20.6 - - + +
412A TYR* 1.3 85.0 - - + +
414A ARG* 1.3 75.7 + - + +
415A ALA* 3.1 1.7 + - - -
745A ASN* 4.9 7.9 - - + +
747A THR 3.4 26.9 - - - +
748A TYR* 4.4 3.6 - - + -
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Residues in contact with ARG 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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384A GLU* 2.9 27.6 + - + +
385A LEU* 3.0 47.2 + - - +
387A PRO* 3.4 24.6 - - - +
397A PHE* 3.8 31.1 - - + +
398A LEU 3.2 14.0 + - - +
399A ASP* 2.9 18.5 + - - +
412A TYR 3.7 0.2 + - - -
413A PRO* 1.3 75.6 - - + +
415A ALA* 1.3 63.0 + - - +
416A LEU 3.3 4.0 - - - -
743A SER* 2.9 49.0 + - - +
744A TYR* 3.9 2.0 - - - +
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Residues in contact with ALA 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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328A LEU* 4.6 0.2 - - + -
382A THR* 3.6 38.0 - - - +
383A HIS 4.5 1.6 - - - +
385A LEU* 3.9 7.5 - - - +
398A LEU 2.8 8.2 + - - +
400A THR* 3.6 25.8 - - + -
412A TYR* 4.0 9.2 - - + +
413A PRO 3.1 1.2 + - - -
414A ARG* 1.3 75.5 - - - +
416A LEU* 1.3 63.4 + - + +
454A THR* 2.8 24.3 + - - -
455A THR 4.4 1.0 + - - -
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Residues in contact with LEU 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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326A PHE* 4.0 26.9 - - + -
328A LEU* 4.1 23.6 - - + -
334A LEU* 3.9 27.1 - - + -
385A LEU* 3.4 7.0 - - - +
397A PHE* 3.5 2.6 - - - +
398A LEU* 2.8 49.0 + - + +
399A ASP 4.7 1.6 - - - +
400A THR* 4.4 10.5 - - - -
414A ARG 4.2 1.0 - - - -
415A ALA* 1.3 91.0 - - + +
417A CYS* 1.3 64.8 + - - +
452A LEU* 4.4 8.5 - - + -
453A ARG 3.3 11.7 - - - +
454A THR* 4.5 2.9 - - - +
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Residues in contact with CYS 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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385A LEU* 3.6 4.5 - - + +
391A CYS* 2.1 50.3 - - + -
395A ALA* 4.2 3.1 - - + -
396A THR 3.1 12.3 - - - +
397A PHE* 3.9 9.9 - - + -
398A LEU* 4.8 2.2 - - - +
416A LEU* 1.3 75.9 - - - +
418A LEU* 1.3 62.0 + - - +
419A PHE* 3.7 15.5 - - - -
451A VAL 3.7 0.3 - - - +
452A LEU* 3.5 7.3 - - - +
453A ARG* 2.9 44.2 + - - -
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Residues in contact with LEU 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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310A PHE* 3.6 36.6 - - + -
312A LEU* 4.0 21.3 - - + -
317A VAL* 3.7 26.9 - - + -
324A PHE* 4.9 4.5 - - + -
326A PHE* 5.2 0.4 - - + -
395A ALA* 3.6 0.2 - - - -
396A THR* 2.8 35.5 + - - +
398A LEU* 5.5 3.1 - - + -
417A CYS* 1.3 74.8 - - - +
419A PHE* 1.3 62.3 + - - +
450A LEU* 3.7 24.2 - - + -
451A VAL 3.2 16.6 - - - +
452A LEU* 3.8 27.6 - - + -
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Residues in contact with PHE 419 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A PHE* 4.0 5.8 - - - -
392A PRO* 3.5 40.6 - - + -
394A THR* 5.1 2.0 - - - +
395A ALA* 3.6 20.9 - - + +
417A CYS* 3.7 32.1 - - - -
418A LEU* 1.3 77.4 - - - +
420A GLU* 1.3 61.5 + - - +
421A MET* 3.8 31.2 - - + -
449A VAL 3.7 0.7 - - - +
450A LEU* 3.5 6.8 - - - -
451A VAL* 2.7 73.0 + - + -
453A ARG* 3.8 20.9 - - - -
424B GLY 4.0 2.9 - - - -
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Residues in contact with GLU 420 (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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302A LEU* 4.0 7.6 - - - +
304A GLN* 4.5 8.9 + - - +
309A ARG* 2.9 53.9 + - - +
310A PHE* 4.0 14.9 - - + -
319A TYR* 2.8 36.1 + - + +
394A THR* 4.9 3.1 + - - -
419A PHE* 1.3 76.8 - - - +
421A MET* 1.3 63.4 + - - +
448A GLN* 3.4 13.3 - - + +
449A VAL 3.3 11.9 - - - +
450A LEU* 4.4 1.6 - - + +
300B PRO* 3.3 34.4 - - + +
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Residues in contact with MET 421 (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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302A LEU* 3.9 11.4 - - + -
419A PHE* 3.8 27.6 - - + -
420A GLU* 1.3 76.2 - - - +
422A PRO* 1.3 96.2 - - + +
423A THR* 3.4 6.8 + - + -
448A GLN* 3.1 6.0 - - - +
449A VAL* 2.9 49.4 + - + +
451A VAL* 4.4 5.4 - - + -
453A ARG* 6.2 0.2 - - - -
421B MET* 4.7 2.7 - - + -
422B PRO 4.1 8.7 - - - +
423B THR* 3.6 31.2 - - - +
424B GLY* 4.0 7.6 - - - +
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Residues in contact with PRO 422 (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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302A LEU* 3.3 34.3 - - + -
420A GLU 4.6 0.7 - - - +
421A MET* 1.3 103.0 - - + +
423A THR* 1.3 62.8 + - - +
424A GLY* 3.5 5.5 + - - +
446A LYS* 4.3 13.9 - - - +
447A GLY 3.3 14.4 - - - +
448A GLN* 3.1 7.3 - - - +
300B PRO* 3.7 21.5 - - + +
301B ARG* 4.5 4.7 - - - -
302B LEU* 4.5 12.5 - - + +
421B MET* 4.1 5.6 - - + +
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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