Contacts of the strand formed by residues 444 - 457 (chain D) in PDB entry 5IG3
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 PRO 444 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437D TYR 3.3 7.4 - - - +
438D LEU* 3.6 7.6 - - + -
442D GLY 3.9 4.9 - - - +
443D ILE* 1.3 96.6 - - + +
445D ARG* 1.3 67.7 + - - +
397F PHE* 3.8 23.3 - - + +
398F TYR* 4.0 23.9 - - + -
401F ASN* 4.9 16.6 - - + -
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Residues in contact with ARG 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436D GLN* 3.4 3.8 - - - +
437D TYR* 2.9 65.9 + - + +
439D ASP* 3.0 29.1 + - + +
443D ILE* 3.8 35.2 - - - +
444D PRO* 1.3 82.8 + - - +
446D THR* 1.3 62.1 + - - +
397F PHE* 5.0 0.3 - - - -
398F TYR* 5.3 2.0 - - - -
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Residues in contact with THR 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434D ILE* 3.5 20.1 - - - +
435D THR 3.2 5.6 + - - -
436D GLN* 4.6 3.0 - - - +
437D TYR* 4.3 3.2 + - - -
445D ARG* 1.3 76.6 - - - +
447D ALA* 1.3 63.6 + - - +
382F PRO 4.6 0.4 - - - +
383F GLU* 3.2 38.8 + - + +
385F LEU* 3.7 26.6 - - + +
398F TYR* 4.0 11.9 - - - +
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Residues in contact with ALA 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433D ARG 3.6 0.9 - - - +
434D ILE* 3.3 5.7 - - - +
435D THR* 2.9 39.6 + - - +
437D TYR* 4.1 19.7 - - + +
446D THR* 1.3 76.2 + - - +
448D GLN* 1.3 60.5 + - - +
472D ALA* 4.0 20.9 - - + -
385F LEU* 3.6 5.8 - - - -
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Residues in contact with GLN 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432D ILE* 3.5 27.2 - - + +
433D ARG 3.5 3.1 - - - -
434D ILE* 3.7 15.3 - - + -
447D ALA* 1.3 74.8 - - - +
449D SER* 1.3 63.7 + - - +
450D GLU* 3.3 21.5 + - - +
471D GLY* 4.0 4.5 - - - -
472D ALA* 3.2 21.5 + - - +
385F LEU* 3.4 28.0 - - + +
387F ASN* 3.1 28.7 + - - +
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Residues in contact with SER 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433D ARG* 2.9 65.1 + - - +
448D GLN* 1.3 78.6 - - - +
450D GLU* 1.3 64.7 + - - +
451D GLU* 3.7 1.4 + - - -
469D ARG* 3.9 17.8 - - - -
470D SER 3.2 13.5 - - - -
472D ALA* 3.9 16.4 - - - -
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Residues in contact with GLU 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431D TYR 3.7 6.3 - - - +
432D ILE* 3.7 23.3 - - + -
448D GLN* 3.3 29.3 + - - +
449D SER* 1.3 72.3 - - - +
451D GLU* 1.3 59.3 + - - +
468D HIS 3.7 1.6 - - - +
469D ARG* 3.3 4.0 - - - -
470D SER* 3.0 55.4 + - - +
471D GLY* 4.4 2.9 + - - -
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Residues in contact with GLU 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358D ILE* 4.7 0.7 - - - +
430D ALA* 3.3 4.9 - - - +
431D TYR* 2.2 83.3 + - + +
433D ARG* 2.6 45.9 + - - -
449D SER 4.1 7.9 - - - +
450D GLU* 1.3 77.4 - - - +
452D THR* 1.3 63.9 + - - +
453D ARG* 3.3 20.9 + - - +
467D PHE* 5.4 1.1 - - + -
468D HIS 3.6 2.7 - - - -
469D ARG* 3.2 28.0 + - + -
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Residues in contact with THR 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428D CYS* 4.2 22.4 - - - -
429D ILE 3.5 4.9 - - - +
430D ALA* 3.9 11.4 - - + +
450D GLU 5.7 0.2 - - - -
451D GLU* 1.3 75.9 + - - +
453D ARG* 1.3 65.8 + - - +
454D VAL* 4.5 9.6 - - + -
466D HIS* 5.9 1.3 - - + -
467D PHE* 3.2 8.5 - - - +
468D HIS* 2.8 51.0 + - + -
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Residues in contact with ARG 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354D THR* 5.0 2.0 - - + -
357D LEU* 3.5 27.8 - - + +
358D ILE* 4.8 2.6 - - - +
361D ILE* 4.1 17.0 - - - +
369D TYR* 4.6 5.9 + - - -
377D MET* 4.4 3.8 - - - +
428D CYS* 3.3 4.5 - - - -
429D ILE* 2.9 39.3 + - + +
431D TYR* 3.5 29.2 + - + +
433D ARG* 5.1 2.0 - - - +
451D GLU* 3.3 24.2 + - - +
452D THR* 1.3 76.3 - - - +
454D VAL* 1.3 63.7 + - - +
455D TRP* 3.5 24.4 + - + +
464D ILE* 3.8 19.6 - - + +
466D HIS 4.1 1.8 - - - -
467D PHE* 3.4 47.1 - - - +
469D ARG* 4.4 3.6 - - - +
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Residues in contact with VAL 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422D MET* 5.4 4.9 - - + -
426D SER* 5.5 2.2 - - - +
427D ALA 3.7 9.9 - - - +
428D CYS* 4.4 11.0 - - + +
452D THR* 4.5 13.2 - - + -
453D ARG* 1.3 75.0 - - - +
455D TRP* 1.3 63.0 + - - +
456D HIS* 6.2 0.2 - - + -
464D ILE* 3.4 4.7 - - - +
465D VAL* 3.0 45.7 + - + +
466D HIS* 3.0 36.8 + - + +
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Residues in contact with TRP 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350D ILE* 3.8 25.6 - - + -
353D VAL* 3.5 40.8 - - + -
354D THR* 3.4 32.3 + - - -
357D LEU* 4.2 13.2 - - + -
372D MET* 3.7 15.9 - - + -
426D SER* 3.6 4.0 + - - -
427D ALA 2.9 35.7 + - - +
429D ILE* 3.7 10.2 - - + +
453D ARG* 3.5 19.1 - - + +
454D VAL* 1.3 76.0 - - - +
456D HIS* 1.3 61.6 + - - +
462D TRP* 3.7 27.8 - - + -
463D GLN 3.4 25.4 - - - -
464D ILE* 3.5 34.8 - - + -
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Residues in contact with HIS 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425D GLU* 2.6 47.2 + - + -
426D SER* 4.4 6.8 - - - +
454D VAL* 6.2 0.2 - - + -
455D TRP* 1.3 75.4 - - - +
457D ARG* 1.3 74.7 + - - +
458D ARG* 3.1 41.4 + - - +
461D LYS 3.5 0.2 - - - +
462D TRP* 3.5 4.2 - - - -
463D GLN* 2.9 30.4 + - - +
465D VAL* 3.8 23.3 - - + -
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Residues in contact with ARG 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D ARG* 3.5 34.2 - - - +
349D GLU* 3.1 27.1 + - - -
424D ASP* 3.6 18.9 + - - +
425D GLU* 2.9 32.8 + - + +
456D HIS* 1.3 85.7 + - - +
458D ARG* 1.3 59.8 - - - +
459D ASP 4.4 0.4 + - - +
460D GLY* 4.0 19.2 - - - +
461D LYS 3.4 19.3 - - - +
462D TRP* 3.3 27.0 - - + +
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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