Contacts of the strand formed by residues 63 - 71 (chain 2) 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 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301 LYS* 5.9 3.3 - - - -
582 HIS* 3.3 8.5 + - - -
592 VAL* 3.0 38.5 + - + -
602 GLY 2.9 19.7 + - - +
612 ASP* 2.9 16.4 + - - +
622 GLU* 1.3 76.7 - - - +
642 PHE* 1.3 61.6 + - - +
882 ASN* 6.0 3.8 - - - -
892 LYS 4.0 2.9 - - - +
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Residues in contact with PHE 64 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412 VAL* 4.0 17.7 - - + -
562 LYS* 4.0 23.8 - - + +
572 VAL 3.2 19.7 - - - +
582 HIS* 3.5 32.1 - + + -
592 VAL* 4.4 1.3 - - - +
622 GLU* 3.5 22.2 - - - -
632 ASP* 1.3 76.4 - - - +
652 VAL* 1.3 67.6 + - - +
882 ASN* 3.6 8.7 + - - +
892 LYS* 3.0 44.4 + - + +
902 ALA 3.6 3.1 - - - -
912 LYS* 3.5 44.9 - - + -
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Residues in contact with VAL 65 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272 LEU* 4.3 13.7 - - + -
352 PHE* 4.9 6.3 - - + -
552 ILE 3.6 1.6 - - - +
572 VAL* 2.9 34.5 + - + +
592 VAL* 4.0 28.0 - - + -
642 PHE* 1.3 78.1 - - - +
662 HIS* 1.3 71.4 + - - +
672 LEU* 3.6 26.6 + - + -
852 TYR* 4.3 6.7 - - + -
862 GLN 3.3 16.2 - - - +
872 THR* 3.9 23.8 - - + -
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Residues in contact with HIS 66 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552 ILE 3.3 4.0 - - - -
562 LYS* 3.0 47.0 + - + +
642 PHE* 4.8 0.7 - - + -
652 VAL* 1.3 80.1 + - - +
672 LEU* 1.3 61.1 + - - +
852 TYR* 3.1 6.2 - - - +
862 GLN* 2.8 43.7 + - - +
892 LYS* 3.7 35.8 - - + +
932 ASP* 3.9 1.4 + - - +
942 GLU 3.3 24.8 + - - -
952 LEU* 3.5 24.1 - - + -
962 THR* 4.6 3.1 - - - -
982 PHE* 3.5 18.4 - + + -
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Residues in contact with LEU 67 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202 ALA* 4.4 9.2 - - + -
232 VAL* 3.9 24.2 - - + -
272 LEU* 4.0 18.2 - - + -
382 PHE* 4.0 11.4 - - + -
532 TYR 3.5 0.5 - - - +
542 PHE* 3.1 9.5 - - - +
552 ILE* 2.8 37.6 + - + +
572 VAL* 3.8 26.9 - - + -
652 VAL* 3.6 25.8 - - + -
662 HIS* 1.3 75.8 - - - +
682 ARG* 1.3 59.3 + - - +
692 VAL* 4.0 13.2 - - + -
822 LEU* 4.2 10.1 - - + -
842 ASN 3.9 2.5 - - - -
852 TYR* 4.1 8.7 - - + -
982 PHE* 3.8 3.0 - - - -
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Residues in contact with ARG 68 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462 GLN* 4.9 2.7 + - - -
522 ASN* 3.5 32.0 + - + +
532 TYR 3.4 3.6 - - - +
542 PHE* 3.6 28.0 - - + -
672 LEU* 1.3 72.4 - - - +
692 VAL* 1.3 58.0 + - - +
822 LEU* 3.6 2.4 - - - +
832 SER* 2.7 50.7 + - - +
842 ASN* 2.9 26.1 + - - +
982 PHE* 2.9 52.1 + - + -
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Residues in contact with VAL 69 (chain 2).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192 ILE* 3.7 30.5 - - + -
232 VAL* 3.9 36.1 - - + -
512 THR 3.6 0.7 - - - +
522 ASN* 3.4 6.1 - - - -
532 TYR* 2.8 47.6 + - + +
552 ILE* 4.4 6.5 - - + -
672 LEU* 4.1 15.3 - - + -
682 ARG* 1.3 78.1 - - - +
702 PHE* 1.3 62.5 + - - +
712 GLN 3.8 0.2 + - - -
802 LEU* 4.0 17.3 - - + -
812 THR 3.4 10.3 - - - +
822 LEU* 4.4 2.2 - - + -
832 SER* 4.4 0.7 - - - -
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Residues in contact with PHE 70 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482 VAL* 3.8 16.2 - - + -
492 ALA 3.2 27.4 - - - -
512 THR 3.7 3.1 - - - -
522 ASN* 3.4 20.9 - - - +
692 VAL* 1.3 73.8 - - - +
712 GLN* 1.3 70.9 + - - +
722 SER* 3.6 26.9 + - - -
762 GLU* 6.0 1.1 - - - -
792 PRO 4.5 1.2 - - - +
802 LEU* 3.6 5.2 - - - -
812 THR* 2.8 45.2 + - + +
832 SER* 3.5 19.1 + - - +
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Residues in contact with GLN 71 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192 ILE* 4.6 6.2 - - - +
502 GLY* 3.3 2.3 - - - -
512 THR* 2.8 57.6 + - - +
532 TYR* 3.5 38.0 + - + -
692 VAL 3.8 0.2 + - - -
702 PHE* 1.3 76.2 - - - +
722 SER* 1.3 73.5 + - - +
742 PRO* 5.9 3.8 - - - +
792 PRO 6.1 0.2 - - - -
802 LEU* 3.6 26.9 - - + +
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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