Contacts of the strand formed by residues 448 - 456 (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 GLN 448 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A ARG* 3.7 15.7 - - - +
319A TYR* 4.0 5.2 - - - +
420A GLU* 3.4 17.3 - - - +
421A MET 3.1 8.5 - - - -
422A PRO* 3.1 23.5 - - - -
423A THR* 4.0 1.4 + - - +
427A LEU* 5.5 1.1 - - - +
446A LYS* 3.5 26.7 + - + +
447A GLY* 1.3 79.0 - - - +
449A VAL* 1.3 70.5 + - - +
470A TYR* 4.6 0.9 - - - -
471A PRO* 3.2 26.0 - - + +
712A ASP* 5.2 2.7 - - - +
299B GLY* 3.6 7.9 - - - +
300B PRO* 2.9 47.5 + - - +
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Residues in contact with VAL 449 (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 TYR* 4.1 6.3 - - - -
419A PHE 3.7 0.7 - - - +
420A GLU* 3.3 2.1 - - - -
421A MET* 2.9 53.8 + - + +
423A THR* 3.4 20.9 - - + -
448A GLN* 1.3 76.0 - - - +
450A LEU* 1.3 59.2 + - - +
451A VAL* 4.0 10.0 + - + -
468A ILE* 3.9 13.2 - - + -
469A PHE 3.7 5.4 - - - +
470A TYR* 3.1 51.4 - - + +
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Residues in contact with LEU 450 (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* 3.4 33.7 - - + -
317A VAL* 3.9 19.1 - - + -
319A TYR* 3.5 46.5 - - + -
324A PHE* 4.0 18.4 - - + -
418A LEU* 3.7 21.3 - - + -
419A PHE 3.5 11.9 - - - +
420A GLU* 4.4 2.5 - - + +
449A VAL* 1.3 72.1 - - - +
451A VAL* 1.3 59.7 + - - +
467A PHE 3.9 0.7 - - - +
468A ILE* 3.2 5.9 - - - +
469A PHE* 2.8 42.4 + - + +
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Residues in contact with VAL 451 (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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417A CYS 3.7 1.0 - - - +
418A LEU* 3.2 8.5 - - - -
419A PHE* 2.7 73.9 + - + +
421A MET* 4.4 6.5 - - + -
449A VAL* 4.3 17.7 - - + -
450A LEU* 1.3 77.4 - - - +
452A LEU* 1.3 65.5 + - - +
453A ARG* 4.2 3.4 - - + +
466A ASP* 3.9 32.3 - - + +
467A PHE 3.6 2.7 - - - +
468A ILE* 3.9 14.6 - - + -
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Residues in contact with LEU 452 (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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324A PHE* 4.4 6.3 - - + -
326A PHE* 3.7 36.6 - - + -
334A LEU* 4.1 23.4 - - + +
336A VAL* 3.5 31.6 - - + -
398A LEU* 5.9 1.3 - - + -
416A LEU* 4.4 15.7 - - + -
417A CYS 3.5 12.8 - - - +
418A LEU* 3.8 21.9 - - + +
450A LEU* 4.3 0.6 - - - +
451A VAL* 1.3 70.8 - - - +
453A ARG* 1.3 60.2 + - - +
465A TRP 3.7 0.7 - - - +
466A ASP* 3.3 3.3 - - - -
467A PHE* 2.8 46.7 + - + +
469A PHE* 4.8 5.8 - - + -
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Residues in contact with ARG 453 (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 LEU* 4.5 3.4 - - - -
385A LEU* 4.4 8.4 - - + +
390A ASP 2.7 33.7 + - - -
391A CYS* 4.1 9.4 - - - +
416A LEU* 3.3 8.1 - - - +
417A CYS* 2.9 42.8 + - - +
419A PHE* 3.8 21.4 - - - -
421A MET* 6.2 0.2 - - - -
451A VAL* 4.2 7.3 - - + +
452A LEU* 1.3 77.2 - - - +
454A THR* 1.3 76.1 + - - +
464A ILE* 3.5 17.7 - - + +
465A TRP 3.2 3.4 - - - -
466A ASP* 2.6 40.7 + - - +
480A HIS* 4.5 0.6 + - - -
424B GLY 2.6 31.3 + - - -
425B VAL* 4.0 15.4 - - - +
426B PRO* 4.5 0.6 - - - +
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Residues in contact with THR 454 (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* 4.0 22.2 - - + +
333A GLY* 6.0 0.2 - - - -
334A LEU* 3.9 26.4 - - + +
382A THR* 3.5 16.6 - - + +
385A LEU* 5.0 1.6 - - - -
415A ALA 2.8 24.0 + - - -
416A LEU* 4.5 6.6 - - - +
453A ARG* 1.3 79.8 - - - +
455A THR* 1.3 76.2 + - - +
465A TRP* 2.8 42.4 + - + +
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Residues in contact with THR 455 (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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381A VAL 4.2 0.7 + - - -
382A THR* 3.4 26.3 - - - +
383A HIS 3.8 23.4 + - - -
385A LEU* 3.4 27.1 - - + +
390A ASP* 5.7 0.7 - - + -
415A ALA 4.4 1.4 + - - -
453A ARG* 5.0 0.7 - - + -
454A THR* 1.3 86.2 + - - +
456A SER* 1.3 64.3 + - - +
457A THR* 4.6 1.0 + - - -
462A ASP* 5.8 0.4 - - - -
463A TYR 3.1 13.7 - - - +
464A ILE* 4.5 15.7 - - + -
465A TRP* 4.0 4.7 - - - -
429B ARG* 4.2 25.1 + - - +
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Residues in contact with SER 456 (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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378A LEU* 3.3 41.8 - - - +
381A VAL* 3.5 9.0 - - - -
455A THR* 1.3 74.6 - - - +
457A THR* 1.3 61.6 + - - +
458A VAL* 3.8 2.8 + - - +
461A TPQ 3.6 1.9 - - - +
462A ASP* 3.4 2.1 - - - -
463A TYR* 2.8 48.4 + - - +
465A TRP* 3.0 24.0 + - - -
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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