Contacts of the helix formed by residues 527 - 546 (chain C) in PDB entry 1P4V
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 527 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525C GLY 3.6 3.7 + - - +
526C ARG* 1.3 74.9 - - - +
528C PRO* 1.3 77.3 - - + +
529C GLN* 3.7 9.1 + - - +
530C GLN* 3.0 27.1 + - + +
531C ALA* 2.8 20.1 + - - +
561C ASN* 5.5 0.4 - - - +
565C GLU* 5.9 2.9 - - - +
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Residues in contact with PRO 528 (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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522C MET* 3.8 23.8 - - + -
526C ARG 4.4 1.6 - - - +
527C THR* 1.3 85.3 - - - +
529C GLN* 1.3 62.6 + - - +
531C ALA* 3.3 2.1 + - - +
532C CYS* 3.0 29.0 + - - -
559C ALA 3.7 13.0 - - - +
561C ASN* 3.6 27.4 - - - +
565C GLU* 3.5 30.5 - - + +
566C TYR 3.6 2.9 - - - +
567C GLY* 3.6 22.2 - - - +
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Residues in contact with GLN 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527C THR* 3.2 8.5 + - - +
528C PRO* 1.3 79.2 - - - +
530C GLN* 1.3 88.7 + - - +
532C CYS* 3.3 4.2 + - - +
533C LYS* 2.9 31.0 + - - +
566C TYR 4.4 3.7 + - - +
567C GLY* 3.7 18.2 - - - -
568C ALA 3.9 19.4 - - - +
569C TYR* 3.9 20.5 - - - -
591C GLY 5.7 0.3 + - - -
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Residues in contact with GLN 530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526C ARG* 3.2 23.6 - - + -
527C THR* 3.0 21.6 + - + +
529C GLN* 1.3 87.1 + - - +
531C ALA* 1.3 65.2 + - - +
533C LYS* 3.2 25.4 + - - +
534C GLU* 2.8 62.3 + - - +
537C GLU* 5.0 0.2 + - - -
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Residues in contact with ALA 531 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C VAL* 3.4 30.8 - - + +
521C LEU* 3.5 22.8 - - + +
522C MET* 3.6 13.5 - - + -
526C ARG* 3.9 8.5 - - + +
527C THR 2.8 17.3 + - - +
528C PRO 3.6 4.5 - - - +
530C GLN* 1.3 77.1 - - - +
532C CYS* 1.3 63.3 + - - +
534C GLU 3.5 0.2 + - - -
535C ALA* 3.2 20.8 + - - +
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Residues in contact with CYS 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C VAL* 4.1 10.5 - - - -
528C PRO 3.0 18.3 + - - -
529C GLN 3.6 6.7 - - - +
531C ALA* 1.3 75.1 - - - +
533C LYS* 1.3 66.7 + - - +
535C ALA* 3.2 3.5 + - - +
536C VAL* 3.0 26.2 + - - +
557C PHE* 3.7 32.0 - - + -
558C ILE 3.9 0.2 - - - -
559C ALA* 3.5 28.9 - - - -
567C GLY 3.9 0.2 - - - -
568C ALA* 3.9 6.7 - - - -
569C TYR* 3.7 19.7 - - + +
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Residues in contact with LYS 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529C GLN* 2.9 22.1 + - - +
530C GLN* 3.2 29.6 + - - +
532C CYS* 1.3 76.5 - - - +
534C GLU* 1.3 57.1 + - - +
536C VAL* 3.1 5.0 + - - +
537C GLU* 2.4 66.1 + - - +
569C TYR* 3.4 50.6 - - + +
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Residues in contact with GLU 534 (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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517C LEU* 5.2 0.4 - - - -
521C LEU* 3.7 17.4 - - + +
526C ARG* 2.8 48.7 + - - +
530C GLN* 2.8 45.0 + - - +
533C LYS* 1.3 75.2 - - - +
535C ALA* 1.3 56.6 - - - +
537C GLU* 3.2 16.4 + - - +
538C ARG* 2.9 29.7 + - - +
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Residues in contact with ALA 535 (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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512C THR* 5.2 0.9 + - - -
514C GLY 4.5 1.1 - - - +
517C LEU* 3.9 25.8 - - + +
518C VAL* 3.5 32.1 - - + -
521C LEU* 4.3 0.6 - - - +
531C ALA 3.2 7.6 + - - +
532C CYS 3.2 6.0 + - - +
534C GLU* 1.3 73.1 - - - +
536C VAL* 1.3 65.9 + - - +
538C ARG* 3.3 3.6 + - - +
539C ILE* 3.2 25.8 + - - +
557C PHE* 3.6 15.7 - - + -
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Residues in contact with VAL 536 (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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532C CYS 3.0 16.5 + - - +
533C LYS 3.4 7.6 - - - +
535C ALA* 1.3 74.6 - - - +
537C GLU* 1.3 59.6 + - - +
539C ILE* 3.0 9.1 + - - +
540C VAL* 2.8 26.0 + - + +
555C VAL* 4.5 4.0 - - + +
557C PHE* 3.9 15.7 - - + -
569C TYR* 3.7 35.9 - - + +
570C CYS* 3.7 24.9 - - - +
571C ILE* 3.9 12.3 - - + +
593C ALA* 3.8 20.6 - - + -
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Residues in contact with GLU 537 (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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530C GLN* 5.0 0.2 + - - -
533C LYS* 2.4 56.0 + - + +
534C GLU* 3.2 24.7 + - - +
536C VAL* 1.3 81.6 - - + +
538C ARG* 1.3 56.3 + - - +
540C VAL* 3.2 9.4 + - + +
541C LYS* 2.9 29.3 + - - +
569C TYR* 4.8 4.6 + - + -
593C ALA* 5.2 6.3 - - + -
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Residues in contact with ARG 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A PHE* 5.5 3.4 - - - -
194A ASP* 4.5 16.9 + - - -
197A ILE* 6.3 0.2 - - - +
216A HIS* 4.2 15.0 - - - -
219A VAL* 6.2 2.0 - - - +
220A GLU* 3.2 27.3 + - - +
223A ASN* 4.1 16.2 - - - +
512C THR* 4.8 6.8 + - + -
517C LEU* 3.7 37.4 - - + +
521C LEU* 5.4 3.8 - - - +
534C GLU 2.9 13.4 + - - +
535C ALA 3.5 10.3 - - - +
536C VAL 3.2 0.2 - - - -
537C GLU* 1.3 75.4 - - - +
539C ILE* 1.3 62.2 + - - +
541C LYS* 3.4 15.9 + - - +
542C ILE* 3.0 42.4 + - + +
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Residues in contact with ILE 539 (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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508C GLU* 3.9 23.1 - - + +
509C VAL* 4.7 0.2 - - - -
512C THR* 3.5 35.2 - - + +
535C ALA 3.2 7.2 + - - +
536C VAL* 3.0 10.4 + - - +
538C ARG* 1.3 76.4 - - - +
540C VAL* 1.3 59.8 + - - +
542C ILE* 3.2 2.2 + - - +
543C VAL* 2.8 43.0 + - + +
555C VAL* 4.0 33.0 - - + -
557C PHE* 4.1 16.2 - - + -
571C ILE* 3.8 22.7 - - + -
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Residues in contact with VAL 540 (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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536C VAL* 2.8 24.3 + - + +
537C GLU* 3.2 11.9 + - + +
539C ILE* 1.3 76.0 - - - +
541C LYS* 1.3 62.5 + - - +
543C VAL* 3.3 2.8 + - - +
544C ASN* 3.0 23.2 + - + +
550C LEU* 3.9 38.4 - - + -
571C ILE* 4.8 2.7 - - + -
593C ALA* 3.8 28.0 - - + -
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Residues in contact with LYS 541 (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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74A TYR* 4.5 5.6 + - - -
194A ASP* 6.0 0.2 + - - -
196A GLU* 2.7 30.7 + - - -
537C GLU 2.9 13.4 + - - +
538C ARG* 3.6 18.3 - - - +
539C ILE 3.2 0.2 - - - -
540C VAL* 1.3 77.3 - - - +
542C ILE* 1.3 64.8 + - - +
544C ASN* 3.2 8.5 + - - +
545C ARG* 2.8 70.8 + - - +
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Residues in contact with ILE 542 (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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74A TYR* 3.5 57.7 - - + -
508C GLU* 5.1 2.2 - - - +
511C ARG* 3.6 21.5 - - - +
512C THR* 3.3 31.0 - - + -
538C ARG* 3.0 24.4 + - + +
539C ILE* 3.7 4.7 - - - +
541C LYS* 1.3 78.6 - - + +
543C VAL* 1.3 68.1 + - - +
545C ARG* 3.2 6.6 + - - +
546C ARG* 2.8 32.9 + - - +
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Residues in contact with VAL 543 (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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508C GLU* 4.2 8.1 - - - +
539C ILE* 2.8 37.2 + - + +
540C VAL 3.6 4.7 - - - +
542C ILE* 1.3 74.1 - - - +
544C ASN* 1.3 63.7 + - - +
546C ARG* 3.2 9.5 + - - +
548C LYS* 3.0 52.0 + - + +
549C ASN 4.1 1.1 - - - +
550C LEU* 3.8 35.2 - - + +
553C ILE* 3.8 25.4 - - + -
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Residues in contact with ASN 544 (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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540C VAL* 3.0 15.2 + - + +
541C LYS* 3.3 10.5 - - - +
543C VAL* 1.3 79.9 - - - +
545C ARG* 1.3 75.7 + - - +
547C GLY* 2.9 20.6 + - - -
548C LYS 4.6 5.2 - - - -
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Residues in contact with ARG 545 (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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73A ASN* 3.0 28.8 + - - +
74A TYR* 3.8 29.3 + - + -
196A GLU* 4.2 16.0 + - - -
541C LYS* 2.8 64.5 + - - +
542C ILE 3.2 4.7 + - - +
544C ASN* 1.3 87.0 + - - +
546C ARG* 1.3 59.7 + - - +
547C GLY 3.2 0.9 + - - -
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Residues in contact with ARG 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 3.6 22.2 - - - +
74A TYR* 3.8 5.6 + - + -
75A ASN* 2.8 31.6 - - - +
96A MET 5.8 2.0 + - - -
508C GLU* 4.1 8.6 + - - -
511C ARG* 3.4 43.4 - - - +
542C ILE* 2.8 38.5 + - + +
543C VAL* 3.8 6.8 - - - +
544C ASN 3.1 0.4 - - - -
545C ARG* 1.3 76.1 - - - +
547C GLY* 1.3 64.5 + - - +
548C LYS* 3.4 43.5 + - + +
553C ILE* 6.1 0.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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