Contacts of the strand formed by residues 63 - 71 (chain 9) 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 ASP 63 (chain 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308 LYS* 5.6 3.4 - - - +
589 HIS* 3.4 6.9 + - - -
599 VAL* 2.9 37.9 + - + -
609 GLY 2.9 21.7 + - - +
619 ASP* 3.0 11.1 + - - +
629 GLU* 1.3 77.9 - - - +
649 PHE* 1.3 62.0 + - - +
889 ASN* 6.0 2.9 - - - -
899 LYS 4.0 2.9 - - - +
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Residues in contact with PHE 64 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419 VAL* 4.3 17.7 - - + -
569 LYS* 4.0 26.0 - - + +
579 VAL 3.1 20.6 - - - +
589 HIS* 3.5 35.0 - + + -
599 VAL* 4.4 1.5 - - - +
629 GLU* 3.5 24.7 - - - -
639 ASP* 1.3 76.7 - - - +
659 VAL* 1.3 68.5 + - - +
889 ASN 3.7 5.5 + - - -
899 LYS* 3.0 43.3 + - + +
909 ALA 3.7 0.9 - - - -
919 LYS* 3.6 38.4 - - + -
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Residues in contact with VAL 65 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279 LEU* 4.0 18.4 - - + -
359 PHE* 4.9 6.3 - - + -
559 ILE 3.5 1.4 - - - +
579 VAL* 2.8 36.2 + - + +
599 VAL* 4.2 25.3 - - + +
649 PHE* 1.3 79.0 - - - +
669 HIS* 1.3 71.9 + - - +
679 LEU* 3.8 24.9 + - + -
859 TYR* 4.4 5.2 - - + -
869 GLN 3.2 15.3 - - - +
879 THR* 3.8 23.1 - - + -
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Residues in contact with HIS 66 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559 ILE 3.2 3.1 - - - -
569 LYS* 3.0 48.2 + - + +
649 PHE* 4.8 0.4 - - + -
659 VAL* 1.3 80.3 + - - +
679 LEU* 1.3 60.4 + - - +
859 TYR* 3.1 6.6 - - - +
869 GLN* 2.8 48.5 + - - +
899 LYS* 3.6 36.2 - - + +
939 ASP* 3.8 0.4 + - - +
949 GLU 3.4 24.1 + - - -
959 LEU* 3.6 26.1 - - + -
969 THR 4.5 3.6 - - - -
989 PHE* 3.4 14.5 - - + -
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Residues in contact with LEU 67 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209 ALA* 4.4 7.2 - - + -
239 VAL* 3.7 25.1 - - + -
279 LEU* 4.0 19.1 - - + -
389 PHE* 4.1 11.2 - - + -
539 TYR 3.4 0.2 - - - +
549 PHE* 3.1 9.7 - - - +
559 ILE* 2.8 42.1 + - + +
579 VAL* 3.8 24.5 - - + -
659 VAL* 3.8 23.6 - - + -
669 HIS* 1.3 75.3 - - - +
689 ARG* 1.3 60.1 + - - +
699 VAL* 4.0 9.4 - - + -
829 LEU* 3.9 18.8 - - + -
849 ASN 4.0 2.5 - - - -
859 TYR* 4.3 3.6 - - + -
989 PHE* 3.9 2.8 - - - -
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Residues in contact with ARG 68 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469 GLN* 4.7 4.8 - - - +
529 ASN* 3.5 31.0 + - + +
539 TYR 3.4 2.9 - - - +
549 PHE* 3.6 29.8 - - + -
679 LEU* 1.3 71.6 - - - +
699 VAL* 1.3 58.3 + - - +
829 LEU* 3.5 3.3 - - - +
839 SER* 2.7 51.5 + - - +
849 ASN* 2.9 28.1 + - - +
989 PHE* 2.7 51.9 + - + -
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Residues in contact with VAL 69 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199 ILE* 3.7 30.5 - - + -
239 VAL* 3.8 37.9 - - + -
519 THR 3.5 1.6 - - - +
529 ASN* 3.3 5.5 - - - -
539 TYR* 2.7 45.2 + - + +
559 ILE* 4.5 4.5 - - + -
679 LEU* 4.0 15.7 - - + -
689 ARG* 1.3 80.6 - - - +
709 PHE* 1.3 62.7 + - - +
719 GLN 3.8 0.4 + - - +
809 LEU* 4.0 17.3 - - + -
819 THR 3.4 9.4 - - - +
829 LEU* 4.1 2.7 - - + -
839 SER* 4.5 0.4 - - - -
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Residues in contact with PHE 70 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489 VAL* 3.8 16.8 - - + -
499 ALA 3.3 26.9 - - - -
519 THR 3.5 2.9 - - - -
529 ASN* 3.3 21.3 - - - +
699 VAL* 1.3 73.8 - - - +
719 GLN* 1.3 68.6 + - - +
729 SER* 3.6 27.2 + - - -
799 PRO 4.4 1.6 - - - +
809 LEU* 3.7 4.2 - - - -
819 THR* 2.8 40.2 + - - +
839 SER* 3.6 18.2 + - - +
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Residues in contact with GLN 71 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199 ILE* 5.1 4.9 - - - +
509 GLY* 3.2 5.9 - - - -
519 THR* 2.7 50.8 + - - +
539 TYR* 3.0 36.1 + - + -
699 VAL 3.8 0.8 + - - -
709 PHE* 1.3 77.3 - - - +
729 SER* 1.3 70.8 + - - +
809 LEU* 3.7 27.6 - - + +
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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