Contacts of the strand formed by residues 63 - 71 (chain 4) 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 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584 HIS* 3.3 8.1 + - - -
594 VAL* 2.9 37.7 + - + -
604 GLY 2.9 19.9 + - - +
614 ASP* 3.0 11.3 + - - +
624 GLU* 1.3 76.0 - - - +
644 PHE* 1.3 61.1 + - - +
884 ASN* 5.7 10.6 + - - +
894 LYS 3.9 3.7 - - - +
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Residues in contact with PHE 64 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414 VAL* 4.2 16.8 - - + -
564 LYS* 3.9 24.5 - - + +
574 VAL 3.2 9.4 - - - +
584 HIS* 3.4 45.1 - + + -
594 VAL* 4.1 1.5 - - - +
624 GLU* 3.5 25.8 - - + -
634 ASP* 1.3 77.6 - - - +
654 VAL* 1.3 67.7 + - - +
884 ASN 3.5 9.0 + - - -
894 LYS* 3.0 43.9 + - + +
914 LYS* 3.4 44.2 - - + -
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Residues in contact with VAL 65 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274 LEU* 4.3 15.9 - - + -
354 PHE* 4.7 6.1 - - + -
384 PHE* 5.6 0.2 - - + -
554 ILE 3.6 1.2 - - - +
574 VAL* 2.8 34.9 + - + +
594 VAL* 4.0 26.4 - - + +
644 PHE* 1.3 78.3 - - - +
664 HIS* 1.3 72.6 + - - +
674 LEU* 3.6 27.1 - - + -
854 TYR* 4.2 9.2 - - + -
864 GLN 3.2 17.3 - - - +
874 THR* 4.3 15.9 - - + -
884 ASN 5.2 0.2 - - - +
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Residues in contact with HIS 66 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554 ILE 3.2 3.6 - - - -
564 LYS* 2.9 49.7 + - + +
644 PHE* 4.7 0.4 - - + -
654 VAL* 1.3 81.2 + - - +
674 LEU* 1.3 61.9 + - - +
854 TYR* 3.1 6.6 - - - +
864 GLN* 2.9 58.0 + - - +
894 LYS* 3.7 26.6 - - + +
934 ASP 3.9 0.6 + - - -
944 GLU 3.4 23.0 + - - -
954 LEU* 3.6 26.6 - - + -
964 THR* 4.7 2.7 - - - -
984 PHE* 3.4 7.8 - + + -
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Residues in contact with LEU 67 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204 ALA* 4.4 10.5 - - + -
234 VAL* 3.9 23.6 - - + -
274 LEU* 4.3 16.4 - - + -
384 PHE* 4.1 11.7 - - + -
534 TYR 3.4 0.4 - - - +
544 PHE* 3.2 8.1 - - - +
554 ILE* 2.8 40.5 + - + +
574 VAL* 3.8 24.5 - - + -
654 VAL* 3.6 24.9 - - + -
664 HIS* 1.3 74.8 - - - +
684 ARG* 1.3 59.6 + - - +
694 VAL* 4.0 9.0 - - + -
824 LEU* 4.0 18.4 - - + -
844 ASN 3.8 2.7 - - - -
854 TYR* 4.1 4.7 - - + -
984 PHE* 3.9 4.1 - - - -
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Residues in contact with ARG 68 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464 GLN* 4.7 4.0 + - - +
524 ASN* 3.5 33.9 + - + +
534 TYR 3.4 3.1 - - - +
544 PHE* 3.5 29.7 - - + -
674 LEU* 1.3 72.1 - - - +
694 VAL* 1.3 57.3 + - - +
824 LEU* 3.6 2.6 - - - +
834 SER* 2.7 51.7 + - - +
844 ASN* 2.8 27.9 + - - +
984 PHE* 2.8 49.6 + - + -
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Residues in contact with VAL 69 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194 ILE* 3.7 31.0 - - + -
234 VAL* 3.8 37.9 - - + -
514 THR 3.5 1.9 - - - +
524 ASN* 3.3 4.9 - - - -
534 TYR* 2.8 44.9 + - + +
554 ILE* 4.5 5.4 - - + -
674 LEU* 4.1 15.9 - - + -
684 ARG* 1.3 77.8 - - - +
704 PHE* 1.3 61.6 + - - +
714 GLN 3.8 0.2 + - - -
804 LEU* 3.9 17.3 - - + -
814 THR 3.2 9.2 - - - +
824 LEU* 4.2 3.1 - - + -
834 SER* 4.3 0.9 - - - -
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Residues in contact with PHE 70 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484 VAL* 3.9 16.2 - - + -
494 ALA 3.3 26.9 - - - -
514 THR 3.6 2.9 - - - -
524 ASN* 3.3 21.5 - - - +
694 VAL* 1.3 73.9 - - - +
714 GLN* 1.3 69.1 + - - +
724 SER* 3.6 28.1 + - - -
784 LYS* 6.4 0.2 - - - -
794 PRO 4.4 1.4 - - - +
804 LEU* 3.7 4.0 - - - -
814 THR* 2.8 43.8 + - + +
834 SER* 3.6 16.7 + - - +
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Residues in contact with GLN 71 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154 GLU* 5.6 1.2 - - - +
194 ILE* 4.6 7.8 - - - +
504 GLY* 3.2 7.4 - - - -
514 THR* 2.7 51.9 + - - +
534 TYR* 3.3 36.4 + - + -
694 VAL 3.8 0.2 + - - -
704 PHE* 1.3 75.8 - - - +
724 SER* 1.3 70.2 + - - +
744 PRO* 6.3 1.0 - - - +
804 LEU* 3.5 28.5 - - + +
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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