Contacts of the strand formed by residues 51 - 60 (chain 3) in PDB entry 4N6V
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 51 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453 SER* 3.8 14.1 - - - -
463 GLN 3.4 12.6 - - - +
473 VAL* 4.5 11.6 - - + +
483 VAL* 4.0 1.7 - - - +
503 GLY* 1.3 77.6 + - - -
523 ASN* 1.3 72.3 + - - +
533 TYR* 3.5 35.0 + - + +
693 VAL 3.5 1.9 - - - +
703 PHE* 3.6 2.0 - - - -
713 GLN* 2.8 47.1 + - - +
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Residues in contact with ASN 52 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453 SER* 3.3 2.9 - - - -
463 GLN* 2.8 67.9 + - - +
483 VAL* 3.7 17.2 - - - +
513 THR* 1.3 72.4 - - - +
533 TYR* 1.3 61.3 + - - +
543 PHE* 3.8 12.4 - - + -
683 ARG* 3.6 29.3 + - + +
693 VAL 3.3 3.7 + - - +
703 PHE* 3.2 35.4 - - - +
833 SER* 5.2 0.4 + - - -
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Residues in contact with TYR 53 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153 GLU* 4.3 14.2 + - - -
163 THR* 6.3 0.4 - - + -
193 ILE* 3.7 32.0 - - + +
433 PHE* 4.1 24.0 - + - -
443 LYS 3.6 1.3 - - - -
453 SER* 4.0 20.9 - - - -
513 THR* 3.5 25.7 + - + +
523 ASN* 1.3 72.8 - - - +
543 PHE* 1.3 62.3 + - - +
553 ILE* 4.0 18.8 + - + -
673 LEU 3.4 1.4 - - - +
683 ARG* 3.4 3.8 - - - -
693 VAL* 2.7 47.8 + - + +
713 GLN* 3.4 39.4 + - + -
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Residues in contact with PHE 54 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433 PHE* 3.1 6.6 - - - +
443 LYS* 2.7 50.3 + - + +
463 GLN* 3.7 23.3 - - + -
523 ASN* 3.8 14.8 - - + -
533 TYR* 1.3 74.9 - - - +
553 ILE* 1.3 58.5 + - - +
673 LEU 3.1 4.9 - - - +
683 ARG* 3.4 32.1 - - + -
953 LEU* 3.4 14.7 - - + +
963 THR 4.2 5.4 - - - +
973 TYR* 3.3 36.1 - + + -
983 PHE* 3.2 54.5 - + - -
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Residues in contact with ILE 55 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163 THR* 3.8 24.2 - - + +
193 ILE* 3.6 36.1 - - + -
203 ALA* 4.2 8.7 - - + +
403 ALA* 3.9 7.2 - - + -
423 SER 3.5 10.5 - - - +
433 PHE* 4.2 7.4 - - + -
533 TYR* 4.2 15.9 - - + +
543 PHE* 1.3 80.8 - - - +
563 LYS* 1.3 65.1 + - - +
573 VAL* 3.7 18.9 + - + -
653 VAL 3.7 0.9 - - - +
663 HIS* 3.2 3.8 - - - -
673 LEU* 2.8 44.8 + - + +
693 VAL* 4.4 10.8 - - + -
953 LEU* 4.0 4.8 - - - +
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Residues in contact with LYS 56 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403 ALA* 3.6 2.8 - - - -
413 VAL* 2.9 40.5 + - + +
423 SER* 2.9 31.2 + - - +
553 ILE* 1.3 70.6 - - - +
573 VAL* 1.3 61.6 + - - +
643 PHE* 3.9 19.7 - - + +
653 VAL 3.7 3.6 - - - -
663 HIS* 3.0 35.7 - - + +
893 LYS* 4.4 1.0 - - - +
903 ALA 2.8 28.8 + - - -
913 LYS* 3.6 16.2 - - - +
933 ASP* 2.8 24.7 + - - +
953 LEU* 4.0 11.0 - - + +
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Residues in contact with VAL 57 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203 ALA* 4.3 5.8 - - + -
383 PHE* 3.7 28.3 - - + -
393 LYS 3.5 24.5 - - - +
403 ALA* 4.2 3.8 - - - +
553 ILE* 3.7 19.1 - - + +
563 LYS* 1.3 79.6 - - - +
583 HIS* 1.3 66.4 + - - +
593 VAL* 3.6 1.4 + - + +
643 PHE* 3.2 8.8 - - - -
653 VAL* 2.8 45.0 + - + +
673 LEU* 3.8 27.4 - - + -
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Residues in contact with HIS 58 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373 VAL* 3.5 21.6 - - + +
383 PHE* 3.3 7.3 + - - -
393 LYS* 2.8 50.3 + - + +
413 VAL* 4.5 5.6 - - + +
563 LYS 4.3 0.2 - - - -
573 VAL* 1.3 70.1 - - - +
593 VAL* 1.3 58.2 + - - +
603 GLY* 3.4 20.4 + - - -
613 ASP 3.5 2.2 + - - -
623 GLU* 3.1 33.9 - - + -
633 ASP 3.4 9.5 + - - -
643 PHE* 3.5 32.9 - + + -
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Residues in contact with VAL 59 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333 LYS* 6.3 0.4 - - - +
353 PHE* 3.5 32.7 - - + -
363 PRO* 3.0 22.9 - - - +
373 VAL* 3.2 12.6 - - - +
383 PHE* 4.0 14.4 - - + -
573 VAL* 3.9 2.0 - - + +
583 HIS* 1.3 78.6 - - - +
603 GLY* 1.3 57.5 + - - +
633 ASP* 2.9 35.3 + - + +
643 PHE 4.6 0.2 - - - -
653 VAL* 3.7 37.2 - - + -
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Residues in contact with GLY 60 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363 PRO* 4.5 7.9 - - - -
373 VAL* 2.9 20.0 - - - +
583 HIS* 3.4 9.2 - - - -
593 VAL* 1.3 80.3 - - - +
613 ASP* 1.3 71.1 + - - +
633 ASP* 2.9 28.4 + - - +
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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