Contacts of the strand formed by residues 63 - 71 (chain 5) 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 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585 HIS* 3.1 10.0 + - - -
595 VAL* 3.0 35.6 + - + +
605 GLY 3.0 13.7 + - - +
615 ASP* 2.9 10.7 + - - +
625 GLU* 1.3 78.4 - - - +
645 PHE* 1.3 62.8 + - - +
885 ASN* 4.9 15.2 + - - -
895 LYS 3.9 4.0 - - - -
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Residues in contact with PHE 64 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415 VAL* 4.4 17.3 - - + -
565 LYS* 3.9 26.2 - - + +
575 VAL 3.1 9.0 - - - +
585 HIS* 3.6 38.6 - + + -
595 VAL* 4.2 2.2 - - - +
625 GLU* 3.8 22.0 - - + -
635 ASP* 1.3 76.2 - - - +
655 VAL* 1.3 70.1 + - - +
885 ASN 3.8 4.3 + - - -
895 LYS* 2.9 43.5 + - + +
905 ALA 3.5 2.7 - - - -
915 LYS* 3.3 46.4 - - + -
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Residues in contact with VAL 65 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275 LEU* 4.2 9.4 - - + -
355 PHE* 4.8 11.7 - - + -
385 PHE* 5.8 0.2 - - + -
555 ILE 3.5 1.0 - - - +
575 VAL* 2.7 39.9 + - + +
595 VAL* 4.4 21.9 - - + +
645 PHE* 1.3 77.9 - - - +
665 HIS* 1.3 77.4 + - - +
675 LEU* 3.7 21.8 - - + -
855 TYR* 4.3 8.3 - - + -
865 GLN 3.3 13.5 - - - +
875 THR* 3.9 22.0 - - + -
885 ASN 5.0 0.2 - - - +
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Residues in contact with HIS 66 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555 ILE 3.2 3.8 - - - -
565 LYS* 2.7 51.8 + - + +
645 PHE* 4.8 0.4 - - + -
655 VAL* 1.3 78.0 - - - +
675 LEU* 1.3 60.6 + - - +
855 TYR* 3.1 7.8 - - - +
865 GLN* 2.9 51.3 + - + +
895 LYS* 3.7 26.7 - - + +
935 ASP* 4.0 0.4 + - - +
945 GLU 3.4 21.8 + - - -
955 LEU* 3.7 22.4 - - + -
965 THR 4.4 4.0 - - - -
985 PHE* 3.7 17.3 - + + -
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Residues in contact with LEU 67 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205 ALA* 4.0 16.6 - - + -
235 VAL* 3.9 23.1 - - + -
275 LEU* 3.8 20.2 - - + -
385 PHE* 4.2 6.7 - - + -
535 TYR 3.6 0.4 - - - +
545 PHE* 3.2 9.4 - - - +
555 ILE* 2.8 39.6 + - + +
575 VAL* 3.5 27.8 - - + -
655 VAL* 3.7 21.1 - - + -
665 HIS* 1.3 75.5 - - - +
685 ARG* 1.3 60.6 + - - +
695 VAL* 4.0 13.9 - - + -
825 LEU* 4.4 9.9 - - + -
845 ASN 3.9 2.9 - - - -
855 TYR* 4.4 7.0 - - + -
985 PHE* 4.1 2.7 - - - -
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Residues in contact with ARG 68 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465 GLN* 5.3 2.2 - - - +
525 ASN* 3.5 28.5 + - + +
535 TYR 3.9 1.8 - - - -
545 PHE* 3.4 30.4 - - + -
675 LEU* 1.3 73.0 - - - +
695 VAL* 1.3 63.6 + - - +
825 LEU* 3.2 7.1 - - - +
835 SER* 2.9 46.7 + - - +
845 ASN* 2.9 24.9 + - - +
985 PHE* 3.0 45.2 + - + -
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Residues in contact with VAL 69 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195 ILE* 3.6 31.0 - - + -
235 VAL* 4.1 25.4 - - + -
515 THR 3.6 0.5 - - - +
525 ASN* 3.5 5.2 - - - -
535 TYR* 2.8 46.0 + - + +
555 ILE* 4.6 4.3 - - + -
675 LEU* 4.0 17.9 - - + -
685 ARG* 1.3 80.5 - - - +
705 PHE* 1.3 62.7 + - - +
715 GLN 3.7 0.4 + - - +
805 LEU* 4.1 23.6 - - + -
815 THR 3.5 8.5 - - - +
825 LEU* 4.7 1.6 - - + -
835 SER* 4.5 0.7 - - - -
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Residues in contact with PHE 70 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485 VAL* 4.2 7.4 - - + -
495 ALA 3.2 28.5 - - - -
505 GLY* 3.9 5.4 - - - -
515 THR 3.7 5.8 - - - -
525 ASN* 3.4 21.3 - - - +
695 VAL* 1.3 74.0 - - - +
715 GLN* 1.3 70.0 + - - +
725 SER* 3.9 23.9 + - - -
785 LYS* 6.0 3.6 - - - -
795 PRO 4.6 0.9 - - - +
805 LEU* 3.5 5.7 - - - -
815 THR* 2.8 52.2 + - + +
835 SER* 3.6 13.2 + - - +
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Residues in contact with GLN 71 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155 GLU* 5.3 1.0 - - - +
195 ILE* 4.7 5.2 - - - +
505 GLY* 3.1 3.8 - - - -
515 THR* 2.9 50.0 + - - +
535 TYR* 3.2 44.6 + - + -
695 VAL 3.7 1.2 + - - -
705 PHE* 1.3 76.1 - - - +
725 SER* 1.3 74.3 + - - +
745 PRO* 5.2 8.3 - - - +
805 LEU* 3.8 22.6 - - + +
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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