Contacts of the strand formed by residues 474 - 486 (chain X) in PDB entry 4HSC
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 VAL 474 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473X TYR* 1.3 74.5 - - - +
475X ALA* 1.3 65.4 + - - +
505X SER* 3.4 34.1 - - - +
506X LYS 3.6 8.1 - - - +
507X THR* 3.7 20.6 - - + -
529X GLU* 3.2 4.2 - - - -
530X CYS* 3.1 37.5 + - + +
538X TRP* 4.1 9.7 - - + -
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Residues in contact with ALA 475 (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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469X HIS* 3.5 25.7 - - + +
473X TYR* 4.0 5.6 - - + -
474X VAL* 1.3 74.5 - - - +
476X GLN* 1.3 65.7 + - - +
477X TYR* 4.8 5.4 - - + -
504X TYR 3.6 0.9 - - - +
505X SER* 3.4 4.7 - - - -
506X LYS* 2.8 34.3 + - + +
528X ARG 3.2 9.9 - - - +
557X ILE* 3.8 23.1 - - + -
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Residues in contact with GLN 476 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475X ALA* 1.3 79.0 - - - +
477X TYR* 1.3 65.1 + - - +
503X TRP* 3.3 38.5 + - + +
504X TYR 3.9 5.2 - - - -
505X SER* 3.3 24.9 + - - +
526X MET* 4.8 0.4 - - - +
527X ALA* 3.4 3.3 - - - +
528X ARG* 2.7 74.6 + - + +
538X TRP* 3.4 28.3 - - + -
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Residues in contact with TYR 477 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467X LEU* 4.1 31.1 - - + +
468X SER 4.3 2.8 + - - -
469X HIS* 3.4 19.9 + - - +
475X ALA* 4.8 5.6 - - + -
476X GLN* 1.3 78.6 - - - +
478X GLU* 1.3 59.8 + - - +
479X ILE* 4.1 13.7 - - + -
499X TRP* 3.9 26.6 - + + -
501X ASN 4.5 0.2 - - - +
502X ASN* 3.4 4.9 - - - -
503X TRP* 2.9 28.1 + - - +
504X TYR 4.8 1.4 + - - -
506X LYS* 4.5 11.4 - - + -
510X PHE* 4.1 19.6 - + - -
525X ILE* 5.4 0.9 - - + -
526X MET* 3.0 11.4 - - - +
527X ALA* 3.5 26.5 - - + -
555X VAL* 4.9 8.7 + - + -
557X ILE* 3.3 30.6 - - + +
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Residues in contact with GLU 478 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477X TYR* 1.3 72.4 - - - +
479X ILE* 1.3 61.9 + - - +
480X LEU* 3.4 31.8 + - + +
502X ASN* 3.6 9.2 - - - +
503X TRP* 3.7 36.0 + - + +
524X ARG* 3.7 2.1 - - - +
525X ILE* 3.6 2.4 - - - -
526X MET* 2.8 58.2 + - + +
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Residues in contact with ILE 479 (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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465X ILE* 4.2 20.0 - - + -
467X LEU* 3.8 27.6 - - + -
477X TYR* 4.1 13.9 - - + -
478X GLU* 1.3 77.7 - - - +
480X LEU* 1.3 63.9 + - - +
481X TRP* 3.9 20.7 - - + -
498X ARG* 3.8 0.5 - - - -
499X TRP* 3.2 33.1 + - + -
502X ASN* 2.8 18.8 + - - +
514X ILE* 3.6 27.4 - - + -
523X ILE* 5.6 1.3 - - + -
524X ARG 3.3 7.0 - - - +
525X ILE* 4.3 19.3 - - + -
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Residues in contact with LEU 480 (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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478X GLU* 3.4 42.6 - - + +
479X ILE* 1.3 78.8 - - - +
481X TRP* 1.3 67.6 + - - +
497X ARG 3.6 15.0 - - - +
498X ARG* 4.6 12.6 - - + +
502X ASN* 4.4 8.7 - - - +
523X ILE* 3.4 1.7 - - - +
524X ARG* 2.7 75.9 + - + +
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Residues in contact with TRP 481 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465X ILE* 5.1 0.2 - - + -
479X ILE* 3.9 20.0 - - + -
480X LEU* 1.3 87.3 - - - +
482X ASP* 1.3 65.9 + - - +
483X GLU* 4.2 1.6 + - + +
497X ARG* 2.7 77.4 + - + +
498X ARG 4.0 8.3 - - - -
499X TRP* 3.7 27.8 - - - -
514X ILE* 3.9 20.6 - - + -
515X PRO 4.0 9.4 - - - -
516X LEU* 3.1 32.1 - - + +
517X GLY 4.8 0.2 - - - +
520X SER* 3.4 29.5 + - - -
521X ARG 3.9 6.5 - - - +
522X ASN 3.4 8.5 - - - -
523X ILE* 3.9 17.3 - - + -
524X ARG* 3.5 2.9 + - - +
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Residues in contact with ASP 482 (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 TRP* 1.3 82.1 - - - +
483X GLU* 1.3 63.8 + - - +
484X ILE* 3.9 2.9 - - + +
494X ILE* 3.8 23.7 - - + +
495X THR 3.4 2.0 - - - -
496X LYS* 3.7 28.6 - - - +
520X SER* 3.3 5.4 - - - -
521X ARG* 2.7 47.8 + - + +
522X ASN* 2.8 30.7 - - + +
524X ARG* 3.9 5.5 + - - -
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Residues in contact with GLU 483 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481X TRP* 4.2 2.4 + - - +
482X ASP* 1.3 75.7 - - - +
484X ILE* 1.3 63.3 + - - +
485X ASN* 3.8 5.9 + - - +
493X VAL 3.9 0.3 - - - +
494X ILE* 3.7 1.3 - - - -
495X THR* 2.7 57.8 + - - +
497X ARG* 3.1 40.5 + - - -
517X GLY* 4.7 9.5 + - - -
519X ASN* 3.5 27.4 - - - +
520X SER* 4.2 9.0 - - - +
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Residues in contact with ILE 484 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146X PHE* 3.7 14.8 - - + -
148X VAL* 5.7 1.6 - - + -
460X TYR* 5.8 6.3 - - + -
482X ASP* 5.1 3.6 - - + -
483X GLU* 1.3 73.4 - - - +
485X ASN* 1.3 60.0 + - - +
486X TYR* 3.9 21.8 - - - +
492X GLU* 4.7 6.1 - - + -
493X VAL 4.0 2.9 - - - -
494X ILE* 4.5 9.6 - - + +
519X ASN* 2.9 50.0 + - + +
520X SER 5.6 0.7 - - - +
521X ARG* 3.2 63.3 - - + +
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Residues in contact with ASN 485 (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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139X GLY 5.3 3.1 - - - +
141X LYS* 2.8 24.8 + - - +
146X PHE* 4.3 7.1 - - - -
483X GLU* 4.1 10.7 + - - +
484X ILE* 1.3 78.6 + - - +
486X TYR* 1.3 77.5 + - - +
487X ASP* 6.1 0.2 - - - +
492X GLU* 3.4 5.0 - - - +
493X VAL* 2.9 39.5 + - + +
495X THR* 5.3 4.6 + - - -
519X ASN* 2.8 24.4 + - - +
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Residues in contact with TYR 486 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137X LYS* 3.8 56.6 + - + +
138X GLU* 4.0 7.5 - - - -
139X GLY* 3.6 27.4 + - - +
146X PHE* 4.1 21.8 - + - -
148X VAL* 4.1 17.6 - - + +
484X ILE* 3.9 20.0 - - + +
485X ASN* 1.3 87.8 + - - +
487X ASP* 1.3 73.9 + - - +
490X GLY 3.9 11.9 - - - +
491X LYS 3.2 6.1 - - - +
492X GLU* 3.8 33.9 + - + -
493X VAL* 4.5 1.8 - - - +
521X ARG* 5.3 0.9 + - - -
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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