Contacts of the strand formed by residues 63 - 71 (chain 7) 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 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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587 HIS* 3.3 6.9 + - - -
597 VAL* 2.9 36.4 + - + -
607 GLY 2.9 14.3 + - - +
617 ASP* 2.9 15.9 + - - +
627 GLU* 1.3 82.4 - - - +
647 PHE* 1.3 62.3 + - - +
887 ASN* 5.5 12.7 + - - +
897 LYS 3.9 3.6 - - - +
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Residues in contact with PHE 64 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417 VAL* 4.2 17.3 - - + -
567 LYS* 4.0 23.3 - - + +
577 VAL 3.2 10.1 - - - +
587 HIS* 3.4 42.6 - + + -
597 VAL* 4.4 1.3 - - - +
627 GLU* 3.6 24.7 - - + -
637 ASP* 1.3 76.2 - - - +
657 VAL* 1.3 67.2 + - - +
887 ASN 3.5 9.2 + - - -
897 LYS* 3.0 42.7 + - + +
907 ALA 3.6 1.6 - - - -
917 LYS* 3.4 44.0 - - + -
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Residues in contact with VAL 65 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277 LEU* 4.1 18.8 - - + -
357 PHE* 4.6 7.2 - - + -
387 PHE* 4.3 0.9 - - + -
557 ILE 3.6 0.7 - - - +
577 VAL* 2.9 44.7 + - + -
597 VAL* 3.7 31.6 - - + -
647 PHE* 1.3 77.7 - - - +
667 HIS* 1.3 66.2 + - - +
677 LEU* 3.9 20.6 - - + -
857 TYR* 5.7 0.9 - - + -
867 GLN 3.3 12.3 - - - +
877 THR* 4.2 19.1 - - + -
887 ASN 5.2 0.2 - - - +
897 LYS* 5.0 0.2 - - - -
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Residues in contact with HIS 66 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557 ILE 3.3 2.9 - - - -
567 LYS* 2.9 48.2 + - + +
647 PHE* 4.7 0.2 - - + -
657 VAL* 1.3 81.3 + - - +
677 LEU* 1.3 61.4 + - - +
857 TYR* 3.1 6.6 - - - +
867 GLN* 2.8 59.1 + - - +
897 LYS* 3.6 28.7 - - + +
947 GLU 3.4 23.7 + - - -
957 LEU* 3.5 28.5 - - + -
967 THR* 4.7 2.5 - - - -
987 PHE* 3.5 6.5 - - + -
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Residues in contact with LEU 67 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207 ALA* 4.3 10.3 - - + -
237 VAL* 3.9 24.2 - - + -
277 LEU* 4.1 17.3 - - + -
387 PHE* 4.2 9.0 - - + -
537 TYR 3.4 0.6 - - - +
547 PHE* 3.1 8.5 - - - +
557 ILE* 2.7 44.6 + - + +
577 VAL* 3.8 24.5 - - + -
657 VAL* 3.9 20.2 - - + -
667 HIS* 1.3 77.2 - - - +
687 ARG* 1.3 60.6 + - - +
697 VAL* 4.0 9.0 - - + -
827 LEU* 4.1 19.1 - - + -
847 ASN 3.9 1.8 - - - -
857 TYR* 4.1 7.0 - - + -
987 PHE* 3.9 4.3 - - - -
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Residues in contact with ARG 68 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467 GLN* 4.6 4.4 - - - +
527 ASN* 3.6 34.4 + - + +
537 TYR 3.4 4.0 - - - +
547 PHE* 3.3 36.6 - - + -
677 LEU* 1.3 73.3 - - - +
697 VAL* 1.3 58.7 + - - +
827 LEU* 3.6 3.1 - - - +
837 SER* 2.8 48.6 + - - +
847 ASN* 2.8 30.7 + - + +
987 PHE* 3.1 30.9 + - + -
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Residues in contact with VAL 69 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197 ILE* 3.9 22.0 - - + -
237 VAL* 3.9 36.8 - - + -
517 THR 3.5 1.7 - - - +
527 ASN* 3.3 3.6 - - - -
537 TYR* 2.7 45.8 + - + +
557 ILE* 4.5 4.9 - - + -
677 LEU* 4.1 14.4 - - + -
687 ARG* 1.3 81.1 - - - +
707 PHE* 1.3 62.4 + - - +
717 GLN 3.8 0.3 + - - -
807 LEU* 3.8 28.9 - - + -
817 THR 3.3 9.6 - - - +
827 LEU* 4.3 2.7 - - + -
837 SER* 4.4 1.1 - - - -
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Residues in contact with PHE 70 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487 VAL* 4.0 15.3 - - + -
497 ALA 3.4 26.5 - - - -
517 THR 3.6 2.9 - - - -
527 ASN* 3.3 23.6 - - - +
697 VAL* 1.3 74.1 - - - +
717 GLN* 1.3 69.9 + - - +
727 SER* 3.6 26.8 + - - -
787 LYS* 6.4 0.2 - - + -
797 PRO 4.5 1.4 - - - +
807 LEU* 3.7 4.5 - - - -
817 THR* 2.9 46.7 + - + +
837 SER* 4.0 11.5 + - - +
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Residues in contact with GLN 71 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157 GLU* 5.6 1.6 - - - +
197 ILE* 4.6 7.3 - - - +
507 GLY* 3.2 6.6 - - - -
517 THR* 2.8 50.5 + - - +
537 TYR* 3.2 36.6 + - + -
697 VAL 3.8 1.0 + - - -
707 PHE* 1.3 75.1 - - - +
727 SER* 1.3 68.2 + - - +
747 PRO* 6.2 1.6 - - - +
807 LEU* 3.6 25.3 - - + +
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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