Contacts of the strand formed by residues 63 - 71 (chain 8) 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 8).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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588 HIS* 3.3 9.0 + - - -
598 VAL* 3.0 37.1 + - + -
608 GLY 2.8 16.0 + - - +
618 ASP* 2.8 19.4 + - - +
628 GLU* 1.3 75.3 - - - +
648 PHE* 1.3 62.4 + - - +
888 ASN* 5.7 5.1 - - - +
898 LYS 4.0 3.4 - - - +
309 LYS* 6.0 1.4 - - - -
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Residues in contact with PHE 64 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418 VAL* 4.2 16.8 - - + -
568 LYS* 4.0 23.8 - - + +
578 VAL 3.2 18.4 - - - +
588 HIS* 3.5 33.4 - + + -
598 VAL* 4.2 1.7 - - - +
628 GLU* 3.4 24.7 - - - -
638 ASP* 1.3 75.6 - - - +
658 VAL* 1.3 67.6 + - - +
888 ASN* 3.5 9.2 + - - -
898 LYS* 3.0 43.3 + - + +
908 ALA 3.7 1.3 - - - -
918 LYS* 3.5 41.7 - - + -
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Residues in contact with VAL 65 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278 LEU* 4.3 15.5 - - + -
358 PHE* 4.7 7.0 - - + -
388 PHE* 5.6 0.2 - - + -
558 ILE 3.6 0.9 - - - +
578 VAL* 2.8 35.9 + - + +
598 VAL* 3.7 29.6 - - + -
648 PHE* 1.3 77.1 - - - +
668 HIS* 1.3 73.5 + - - +
678 LEU* 3.8 24.7 - - + -
858 TYR* 4.3 5.8 - - + -
868 GLN 3.2 17.0 - - - +
878 THR* 4.2 19.7 - - + -
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Residues in contact with HIS 66 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558 ILE 3.2 3.8 - - - -
568 LYS* 3.0 46.5 + - + +
648 PHE* 4.8 0.2 - - + -
658 VAL* 1.3 79.6 + - - +
678 LEU* 1.3 60.9 + - - +
858 TYR* 3.2 6.6 - - - +
868 GLN* 2.9 48.1 + - - +
898 LYS* 3.7 30.5 - - + +
938 ASP* 3.9 1.4 + - - +
948 GLU 3.3 23.2 + - - -
958 LEU* 3.5 26.4 - - + -
968 THR* 4.6 4.7 - - - -
988 PHE* 3.5 14.2 - - + -
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Residues in contact with LEU 67 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208 ALA* 4.4 10.1 - - + -
238 VAL* 3.8 24.7 - - + -
278 LEU* 4.1 16.4 - - + -
388 PHE* 4.0 12.3 - - + -
538 TYR 3.5 0.4 - - - +
548 PHE* 3.1 10.4 - - - +
558 ILE* 2.7 42.2 + - + +
578 VAL* 3.9 23.3 - - + -
658 VAL* 3.8 22.7 - - + -
668 HIS* 1.3 74.7 - - - +
688 ARG* 1.3 59.3 + - - +
698 VAL* 4.0 13.2 - - + -
828 LEU* 4.1 15.0 - - + -
848 ASN 3.9 2.2 - - - -
858 TYR* 4.1 5.8 - - + -
988 PHE* 3.8 3.4 - - - -
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Residues in contact with ARG 68 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468 GLN* 5.0 2.1 + - - -
528 ASN* 3.5 32.1 + - + +
538 TYR 3.4 4.3 - - - +
548 PHE* 3.6 29.3 - - + -
678 LEU* 1.3 72.1 - - - +
698 VAL* 1.3 62.2 + - - +
828 LEU* 3.6 3.5 - - - +
838 SER* 2.8 45.6 + - - -
848 ASN* 2.9 27.7 + - - +
988 PHE* 3.0 42.9 + - + -
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Residues in contact with VAL 69 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198 ILE* 3.8 30.1 - - + -
238 VAL* 3.8 37.5 - - + -
518 THR 3.6 1.0 - - - +
528 ASN* 3.3 6.0 - - - -
538 TYR* 2.8 46.6 + - + +
558 ILE* 4.4 5.8 - - + -
678 LEU* 4.1 15.5 - - + -
688 ARG* 1.3 77.0 - - - +
708 PHE* 1.3 62.1 + - - +
718 GLN 3.8 0.2 + - - -
808 LEU* 4.0 18.2 - - + -
818 THR 3.4 10.8 - - - +
828 LEU* 4.4 2.2 - - + -
838 SER* 4.4 0.7 - - - -
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Residues in contact with PHE 70 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488 VAL* 3.8 17.5 - - + -
498 ALA 3.3 27.4 - - - -
508 GLY* 4.3 0.2 - - - -
518 THR 3.7 2.0 - - - -
528 ASN* 3.3 21.5 - - - +
698 VAL* 1.3 75.0 - - - +
718 GLN* 1.3 71.7 + - - +
728 SER* 3.5 26.3 + - - -
798 PRO 4.4 1.2 - - - +
808 LEU* 3.6 4.5 - - - -
818 THR* 2.8 46.4 + - + +
838 SER* 3.5 18.7 + - - +
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Residues in contact with GLN 71 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198 ILE* 4.8 6.6 - - - +
508 GLY* 3.3 2.6 - - - -
518 THR* 2.8 50.6 + - - +
538 TYR* 3.3 37.1 + - + -
698 VAL 3.8 0.6 + - - -
708 PHE* 1.3 75.7 - - - +
728 SER* 1.3 75.3 + - - +
748 PRO* 6.0 3.7 - - - +
808 LEU* 3.5 25.1 - - + +
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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