Contacts of the strand formed by residues 444 - 457 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437C TYR 3.5 6.3 - - - +
438C LEU* 3.6 14.6 - - + -
442C GLY 4.2 0.9 - - - -
443C ILE* 1.3 90.0 - - - +
445C ARG* 1.3 70.0 + - - +
397D PHE* 4.1 17.5 - - + -
398D TYR* 4.1 28.8 - - + -
401D ASN* 5.6 1.6 - - + -
402D LEU* 4.8 25.6 - - + -
473D PRO 5.3 4.3 - - - +
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Residues in contact with ARG 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C GLN* 3.3 5.9 - - - +
437C TYR* 2.9 62.9 + - + +
439C ASP* 3.6 33.1 + - - +
443C ILE* 3.1 29.8 - - - +
444C PRO* 1.3 79.5 + - - +
446C THR* 1.3 65.5 + - - +
397D PHE* 4.8 1.2 - - - -
398D TYR* 5.2 2.5 + - - -
473D PRO 6.0 0.8 + - - -
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Residues in contact with THR 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C ILE* 3.6 19.2 - - - +
435C THR 3.2 7.2 - - - -
436C GLN* 4.6 8.7 - - - +
437C TYR* 4.1 4.4 + - - -
444C PRO 5.9 0.2 - - - +
445C ARG* 1.3 81.9 - - - +
447C ALA* 1.3 63.2 + - - +
382D PRO 4.7 0.4 - - - +
383D GLU* 3.1 42.5 + - + +
385D LEU* 3.7 22.6 - - + +
398D TYR* 4.7 4.5 - - - +
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Residues in contact with ALA 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433C ARG 3.8 0.5 - - - +
434C ILE* 3.3 5.5 - - - +
435C THR* 2.9 37.7 + - - +
437C TYR* 4.1 18.4 - - + +
446C THR* 1.3 76.4 + - - +
448C GLN* 1.3 62.2 + - - +
471C GLY 5.8 0.9 - - - +
472C ALA* 6.3 2.9 - - + -
385D LEU* 3.6 7.4 - - - -
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Residues in contact with GLN 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C ILE* 3.8 28.5 - - + +
433C ARG 3.5 2.7 - - - -
434C ILE* 4.5 4.0 - - + -
447C ALA* 1.3 76.8 - - - +
449C SER* 1.3 60.7 + - - +
450C GLU* 3.4 21.1 + - - +
471C GLY* 2.7 29.5 - - - +
472C ALA* 4.7 0.7 - - - -
385D LEU* 3.2 40.6 - - + +
387D ASN* 3.3 23.1 + - - +
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Residues in contact with SER 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C ILE* 3.6 5.4 - - - +
433C ARG* 2.9 54.5 + - - +
448C GLN* 1.3 76.8 - - - +
450C GLU* 1.3 67.0 + - - +
451C GLU* 3.7 9.9 + - - -
469C ARG* 4.2 9.1 - - - -
470C SER 3.1 15.7 - - - -
472C ALA* 3.8 20.5 - - - +
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Residues in contact with GLU 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C TYR 3.8 5.8 - - - +
432C ILE* 4.4 16.2 - - + -
448C GLN* 3.4 31.4 + - - +
449C SER* 1.3 77.2 - - - +
451C GLU* 1.3 61.8 + - - +
452C THR* 5.6 0.2 - - - -
468C HIS 3.7 1.2 - - - +
469C ARG* 3.4 3.6 - - - -
470C SER* 3.1 52.8 + - - +
471C GLY* 4.5 2.4 + - - -
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Residues in contact with GLU 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430C ALA* 3.4 3.5 - - - +
431C TYR* 2.9 71.6 + - + +
433C ARG* 2.8 52.4 + - + -
449C SER* 3.7 10.9 + - - +
450C GLU* 1.3 78.6 - - - +
452C THR* 1.3 63.1 + - - +
453C ARG* 3.3 15.0 + - - +
467C PHE* 6.0 0.2 - - - -
468C HIS 3.2 4.5 - - - +
469C ARG* 3.4 29.1 + - + -
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Residues in contact with THR 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428C CYS* 4.0 24.0 - - - -
429C ILE 3.5 4.9 - - - +
430C ALA* 3.9 11.3 - - + +
451C GLU* 1.3 76.7 + - - +
453C ARG* 1.3 67.5 + - - +
454C VAL* 4.4 8.7 - - + -
466C HIS* 6.1 1.3 - - + -
467C PHE* 3.1 8.8 - - - +
468C HIS* 2.8 52.3 + - + +
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Residues in contact with ARG 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C THR* 5.1 1.3 - - + -
357C LEU* 3.5 28.0 - - + +
358C ILE* 4.6 0.2 - - - +
361C ILE* 3.8 15.0 - - - +
369C TYR* 4.5 6.9 + - - -
428C CYS* 3.4 5.7 - - - -
429C ILE* 2.9 37.7 + - + +
431C TYR* 3.5 27.0 + - + +
433C ARG* 3.4 15.8 - - - +
451C GLU* 3.3 23.6 + - - +
452C THR* 1.3 76.4 - - - +
454C VAL* 1.3 62.6 + - - +
455C TRP* 3.4 25.7 + - + +
464C ILE* 4.4 10.8 - - + +
466C HIS 4.0 1.8 - - - -
467C PHE* 3.2 48.2 - - - +
469C ARG* 4.4 6.9 - - - +
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Residues in contact with VAL 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422C MET* 5.3 4.7 - - + -
426C SER* 5.6 1.8 - - - +
427C ALA 3.8 9.6 - - - +
428C CYS* 4.4 15.7 - - + +
452C THR* 4.4 9.0 - - + -
453C ARG* 1.3 75.4 - - - +
455C TRP* 1.3 62.2 + - - +
456C HIS* 6.1 0.2 - - + -
464C ILE* 3.5 3.5 - - - +
465C VAL* 2.9 47.2 + - + +
466C HIS* 3.0 37.8 + - + +
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Residues in contact with TRP 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C ILE* 4.3 18.4 - - + -
353C VAL* 3.5 50.7 - - + -
354C THR* 3.7 14.1 + - + -
357C LEU* 4.0 18.6 - - + -
372C MET* 3.7 15.5 - - + -
426C SER* 3.6 3.5 + - - -
427C ALA 2.9 35.8 + - - +
429C ILE* 3.6 23.8 - - + +
453C ARG* 3.4 21.4 - - + +
454C VAL* 1.3 75.2 - - - +
456C HIS* 1.3 62.4 + - - +
462C TRP* 3.8 26.7 - - + -
463C GLN 3.4 14.6 - - - -
464C ILE* 3.5 38.8 - - + -
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Residues in contact with HIS 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C GLU* 2.6 49.1 + - + -
426C SER* 4.7 4.8 - - - -
454C VAL* 6.1 0.2 - - + -
455C TRP* 1.3 77.4 - - - +
457C ARG* 1.3 77.4 + - - +
458C ARG* 3.2 41.3 + - + +
461C LYS 3.6 0.2 - - - +
462C TRP* 3.7 4.0 - - - -
463C GLN* 2.9 28.7 + - - +
465C VAL* 3.7 22.4 - - + -
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Residues in contact with ARG 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346C ARG* 3.4 21.7 - - - +
349C GLU* 2.6 36.4 + - - -
424C ASP* 4.6 6.2 + - - +
425C GLU* 2.9 26.3 + - + +
456C HIS* 1.3 85.7 - - - +
458C ARG* 1.3 60.9 + - - +
459C ASP 4.2 0.9 + - - +
460C GLY* 3.9 19.4 - - - +
461C LYS 3.3 22.6 - - - +
462C TRP* 3.3 36.4 - - + +
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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