Contacts of the strand formed by residues 39 - 47 (chain 3) 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 LYS 39 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173 GLN* 3.5 7.9 - - - +
373 VAL* 5.3 3.8 - - + -
383 PHE* 1.3 75.3 - - - +
403 ALA* 1.3 72.8 + - - +
413 VAL* 3.4 13.7 + - + +
573 VAL* 3.6 3.1 - - - +
583 HIS* 2.8 49.7 + - + +
144 ALA* 4.7 17.7 - - - +
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Residues in contact with ALA 40 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123 ALA* 3.3 12.6 - - + +
163 THR* 3.9 28.5 - - + +
173 GLN* 2.8 34.0 + - - +
203 ALA* 4.4 4.9 - - + -
383 PHE 3.9 0.6 + - - -
393 LYS* 1.3 81.1 - - - +
413 VAL* 1.3 59.5 + - - +
553 ILE* 3.9 10.5 - - + -
563 LYS 3.6 6.3 - - - -
573 VAL* 4.2 5.0 - - - +
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Residues in contact with VAL 41 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113 PRO* 3.7 5.4 - - - +
123 ALA* 2.9 20.3 + - - +
393 LYS* 3.7 20.6 - - + +
403 ALA* 1.3 75.6 - - - +
423 SER* 1.3 67.5 + - - +
563 LYS* 2.9 46.6 + - + +
583 HIS* 4.5 5.4 - - + -
643 PHE* 4.2 19.7 - - + -
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Residues in contact with SER 42 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93 THR* 3.5 17.4 - - - +
103 GLN 3.2 15.5 - - - -
113 PRO* 4.5 1.1 - - - -
123 ALA* 3.6 5.4 - - - +
413 VAL* 1.3 83.4 - - - +
433 PHE* 1.3 66.4 + - - +
553 ILE* 3.5 5.1 - - - +
563 LYS* 2.9 48.7 + - - +
953 LEU* 4.1 3.1 - - - +
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Residues in contact with PHE 43 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93 THR* 3.3 1.3 - - - +
103 GLN* 2.8 77.8 + - + +
113 PRO 3.6 17.3 - - - -
123 ALA* 4.3 0.2 - - - -
133 THR* 4.9 7.9 - - + -
163 THR* 3.5 38.6 - - + -
423 SER* 1.3 79.5 - - - +
443 LYS* 1.3 73.6 + - - +
453 SER* 4.4 10.5 - - - -
533 TYR* 4.1 23.1 - + - -
543 PHE 3.1 13.5 - - - +
553 ILE* 4.2 4.9 - - + -
953 LEU* 3.6 7.0 - - - -
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Residues in contact with LYS 44 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83 ALA* 3.9 20.0 - - - +
93 THR* 3.7 17.9 + - - +
103 GLN* 5.2 1.3 - - - +
433 PHE* 1.3 84.6 - - - +
453 SER* 1.3 60.7 + - - +
533 TYR* 3.6 1.9 - - - -
543 PHE* 2.7 41.3 + - + +
943 GLU* 4.7 7.9 + - - -
953 LEU* 3.1 30.4 + - + +
963 THR* 4.1 5.5 - - - +
973 TYR* 3.6 58.9 - - + +
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Residues in contact with SER 45 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103 GLN* 4.7 6.2 + - - +
433 PHE* 4.1 9.7 - - - -
443 LYS* 1.3 76.7 - - - +
463 GLN* 1.3 62.4 + - - +
473 VAL* 4.2 4.5 - - - +
513 THR* 3.8 20.2 - - - -
523 ASN 3.3 5.2 - - - -
533 TYR* 4.0 15.0 - - - -
973 TYR* 3.4 15.6 + - - -
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Residues in contact with GLN 46 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453 SER* 1.3 77.0 - - - +
473 VAL* 1.3 66.5 + - - +
483 VAL* 3.5 10.8 + - + +
513 THR* 3.4 1.8 - - - -
523 ASN* 2.8 70.3 + - + +
543 PHE* 3.7 17.7 - - + -
683 ARG* 4.7 6.1 - - - +
973 TYR* 3.6 31.8 - - + +
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Residues in contact with VAL 47 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453 SER* 5.6 4.7 - - - +
463 GLN* 1.3 73.5 - - - +
483 VAL* 1.3 78.7 + - - +
503 GLY 3.7 8.7 - - - +
513 THR* 4.4 12.1 - - + +
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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