Contacts of the helix formed by residues 511 - 528 (chain X) in PDB entry 4B3F
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 ASN 511 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498X LEU* 2.8 27.1 + - - +
499X PHE 3.4 15.1 + - - +
500X GLU* 3.7 0.6 - - - +
501X LEU* 4.6 0.4 - - - +
510X GLY* 1.3 76.1 - - - +
512X PRO* 1.3 62.2 - - - +
513X GLY* 3.1 8.3 + - - -
514X GLU* 2.9 49.5 + - + +
515X VAL* 3.1 11.1 + - - +
544X GLN* 3.0 17.6 + - - +
547X LEU* 5.1 1.4 - - - +
580X VAL* 3.2 28.8 + - - +
582X SER* 3.8 3.0 - - - -
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Residues in contact with PRO 512 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499X PHE 4.2 9.4 - - - +
501X LEU* 4.3 23.6 - - + -
510X GLY 4.3 2.2 - - - -
511X ASN* 1.3 83.7 - - - +
513X GLY* 1.3 65.3 + - - +
515X VAL* 3.4 13.5 + - + +
516X ARG* 3.2 31.9 + - - +
547X LEU* 4.6 16.6 - - + -
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Residues in contact with GLY 513 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498X LEU* 3.7 29.8 - - - +
499X PHE 5.3 0.4 + - - -
511X ASN* 3.1 7.9 + - - -
512X PRO* 1.3 79.9 - - - +
514X GLU* 1.3 61.1 + - - +
516X ARG* 3.2 18.1 + - - +
517X LEU* 3.2 22.9 + - - +
643X LEU* 4.8 1.7 - - - +
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Residues in contact with GLU 514 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493X THR* 4.6 9.2 + - - +
498X LEU* 5.2 1.1 - - + +
511X ASN* 2.9 37.0 + - - +
513X GLY* 1.3 73.5 - - - +
515X VAL* 1.3 65.6 + - - +
517X LEU* 3.0 6.1 + - - +
518X VAL* 2.9 27.8 + - - +
544X GLN* 3.6 8.1 - - - +
578X SER* 2.8 18.9 + - - +
579X PHE 3.2 6.6 + - - -
580X VAL* 2.7 39.9 + - - -
581X ARG 4.5 2.1 + - - +
582X SER* 4.8 2.1 - - - -
611X ILE* 3.4 27.8 - - + +
612X CYS* 3.9 14.6 - - - -
613X ASP 4.3 4.9 + - - -
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Residues in contact with VAL 515 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511X ASN 3.1 14.6 + - - +
512X PRO* 3.5 14.8 - - + +
513X GLY 3.3 0.2 - - - -
514X GLU* 1.3 76.7 - - - +
516X ARG* 1.3 54.6 + - + +
518X VAL* 4.1 1.6 - - - +
519X SER* 2.6 34.7 + - - +
544X GLN* 3.6 19.9 - - - +
547X LEU* 3.8 28.7 - - + +
548X LEU* 3.9 22.2 - - + +
551X SER* 3.8 31.4 - - - +
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Residues in contact with ARG 516 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498X LEU* 5.7 3.8 - - - +
512X PRO* 3.2 19.2 + - - +
513X GLY* 3.6 11.9 - - - +
514X GLU 3.1 0.8 - - - -
515X VAL* 1.3 77.0 - - + +
517X LEU* 1.3 66.3 + - - +
519X SER* 3.4 5.9 + - - -
520X LEU* 3.1 30.1 + - + +
643X LEU* 3.6 34.2 - - + +
645X ASP* 3.2 34.7 + - - -
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Residues in contact with LEU 517 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491X VAL* 3.9 16.2 - - + -
493X THR* 3.9 16.4 - - - +
498X LEU* 4.0 8.7 - - + -
513X GLY 3.2 9.1 + - - +
514X GLU* 3.0 7.4 + - - +
516X ARG* 1.3 76.8 - - - +
518X VAL* 1.3 59.1 + - - +
520X LEU* 3.2 6.3 + - - +
521X HIS* 2.9 28.7 + - - +
611X ILE* 4.0 22.0 - - + -
639X ALA* 3.9 22.9 - - + -
642X TYR* 3.3 43.1 - - + -
643X LEU* 3.5 20.0 - - + -
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Residues in contact with VAL 518 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514X GLU 2.9 25.0 + - - +
515X VAL 4.2 0.4 - - - +
517X LEU* 1.3 72.5 - - - +
519X SER* 1.3 58.0 + - - +
521X HIS* 3.7 4.0 - - - +
522X ILE* 2.8 35.1 + - + +
537X VAL* 4.0 27.6 - - + -
548X LEU* 3.6 29.6 - - + -
552X LEU* 4.2 4.7 - - + -
576X ILE* 3.8 22.1 - - + +
578X SER* 4.5 17.5 - - - -
611X ILE* 4.4 11.8 - - + +
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Residues in contact with SER 519 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515X VAL* 2.6 29.3 + - - +
516X ARG* 3.8 7.4 - - - -
517X LEU 3.2 0.6 - - - -
518X VAL* 1.3 72.3 - - - +
520X LEU* 1.3 61.7 + - - +
522X ILE* 3.3 3.8 + - - +
523X GLN* 2.9 30.8 + - - +
551X SER* 4.7 4.5 - - - -
552X LEU* 3.3 35.3 - - - +
555X ARG* 4.0 18.3 + - - -
556X HIS* 5.4 0.5 - - - -
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Residues in contact with LEU 520 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516X ARG* 3.1 16.8 + - + +
517X LEU* 3.5 8.3 - - - +
519X SER* 1.3 78.3 - - - +
521X HIS* 1.3 57.0 + - - +
523X GLN* 3.4 9.6 + - + +
524X ALA* 3.0 23.7 + - - +
642X TYR* 3.7 33.2 - - + +
643X LEU* 3.5 31.6 - - + -
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Residues in contact with HIS 521 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483X GLU* 3.9 26.1 - - + +
489X LEU* 4.3 12.9 - - + +
491X VAL* 5.7 1.1 - - + -
517X LEU 2.9 16.1 + - - +
518X VAL* 4.2 5.2 - - - +
520X LEU* 1.3 73.9 - - - +
522X ILE* 1.3 64.6 + - - +
524X ALA* 3.3 5.7 + - + -
525X LEU* 3.3 42.7 + - + +
576X ILE* 3.7 15.1 - - + +
607X HIS* 3.3 31.9 + + - -
609X ALA* 3.5 21.0 - - + +
611X ILE* 5.3 6.0 - - + +
642X TYR* 4.6 19.0 - + + +
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Residues in contact with ILE 522 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518X VAL* 2.8 29.8 + - + +
519X SER* 3.5 9.0 - - - +
521X HIS* 1.3 72.9 - - - +
523X GLN* 1.3 67.3 - - - +
525X LEU* 3.1 5.2 + - - +
526X VAL* 2.9 30.0 + - + +
532X ALA* 6.3 0.2 - - + -
535X ILE* 4.0 14.8 - - + -
537X VAL* 3.4 26.0 - - + -
552X LEU* 4.8 3.4 - - + -
556X HIS* 3.5 33.0 - - + +
559X LEU* 3.6 15.5 - - + -
576X ILE* 3.4 23.8 - - + +
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Residues in contact with GLN 523 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519X SER 2.9 16.4 + - - +
520X LEU* 3.5 11.0 - - + +
521X HIS 3.2 0.2 - - - -
522X ILE* 1.3 77.9 - - - +
524X ALA* 1.3 57.5 + - - +
526X VAL* 4.3 8.6 - - - +
527X ASP* 2.9 73.2 + - - +
555X ARG* 4.7 13.3 + - - +
556X HIS* 3.2 31.7 + - - -
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Residues in contact with ALA 524 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481X THR* 5.6 0.2 - - - +
483X GLU* 4.2 23.3 - - + +
520X LEU 3.0 13.3 + - - +
521X HIS* 3.4 24.5 - - + +
522X ILE 3.1 0.2 - - - -
523X GLN* 1.3 78.1 - - - +
525X LEU* 1.3 61.5 + - - +
527X ASP* 3.6 4.2 + - - +
528X ALA* 3.3 22.7 + - - +
642X TYR* 6.4 1.1 - - + -
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Residues in contact with LEU 525 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472X LEU* 4.6 15.3 - - + -
481X THR* 5.7 0.2 - - + -
483X GLU* 3.8 22.9 - - + -
484X THR* 4.6 6.5 - - + -
521X HIS* 3.3 42.1 + - + +
522X ILE 3.1 6.4 + - - +
524X ALA* 1.3 74.2 - - - +
526X VAL* 1.3 65.9 + - - +
528X ALA* 3.1 10.2 + - - -
529X GLY 3.2 0.3 + - - -
530X VAL* 3.0 30.6 + - + +
535X ILE* 3.9 24.2 - - + -
574X ALA* 4.4 18.8 - - + -
576X ILE* 4.5 9.9 - - + -
607X HIS* 4.6 5.2 - - + +
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Residues in contact with VAL 526 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522X ILE* 2.9 25.9 + - + +
523X GLN* 4.1 11.0 - - - +
525X LEU* 1.3 75.4 - - - +
527X ASP* 1.3 64.5 + - - +
529X GLY* 3.1 14.9 + - - -
530X VAL 3.5 16.3 + - - +
532X ALA* 4.6 10.1 - - + +
535X ILE* 4.3 9.6 - - + -
556X HIS* 3.8 35.9 - - + +
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Residues in contact with ASP 527 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523X GLN* 2.9 54.4 + - - +
524X ALA* 3.9 4.5 - - - +
526X VAL* 1.3 81.0 - - - +
528X ALA* 1.3 59.6 + - - +
529X GLY 3.3 0.4 - - - -
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Residues in contact with ALA 528 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477X GLY 3.8 2.1 - - - +
478X VAL* 3.6 1.2 - - + -
479X ALA* 2.9 40.9 + - + +
481X THR* 4.1 17.0 - - + +
484X THR* 4.0 24.7 - - + -
524X ALA 3.3 15.2 + - - +
525X LEU* 3.1 7.0 + - - +
527X ASP* 1.3 77.8 - - - +
529X GLY* 1.3 57.3 + - - +
530X VAL 3.7 0.7 - - - -
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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