Contacts of the strand formed by residues 51 - 60 (chain 1) 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 THR 51 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451 SER* 4.0 11.0 - - - -
461 GLN 3.5 11.4 + - - +
471 VAL* 4.7 9.3 - - + +
481 VAL* 3.9 1.7 - - - +
501 GLY* 1.3 77.8 + - - -
521 ASN* 1.3 75.1 + - - +
531 TYR* 3.4 35.2 + - + +
691 VAL 3.5 1.4 - - - +
701 PHE* 3.5 2.0 - - - -
711 GLN* 2.7 50.8 + - - +
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Residues in contact with ASN 52 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441 LYS 3.9 0.5 - - - +
451 SER* 3.4 2.4 - - - -
461 GLN* 2.8 64.9 + - - +
481 VAL* 3.5 18.0 - - - +
511 THR* 1.3 74.1 - - - +
531 TYR* 1.3 61.3 + - - +
541 PHE* 3.9 11.5 + - + -
681 ARG* 3.5 30.6 + - + +
691 VAL 3.2 4.3 + - - +
701 PHE* 3.2 35.8 - - - +
831 SER* 4.9 1.0 + - - -
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Residues in contact with TYR 53 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151 GLU* 4.2 14.2 + - - -
161 THR* 6.3 1.1 - - + -
191 ILE* 4.0 31.6 - - + +
431 PHE* 4.4 17.7 - + - -
441 LYS 3.6 1.3 - - - -
451 SER* 3.5 24.9 - - - -
511 THR* 3.4 27.1 + - + +
521 ASN* 1.3 73.4 - - - +
541 PHE* 1.3 62.4 + - - +
551 ILE* 3.9 16.9 + - + -
671 LEU 3.4 3.3 - - - +
681 ARG* 3.4 1.2 - - - -
691 VAL* 2.7 46.5 + - + +
711 GLN* 3.1 39.1 + - + -
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Residues in contact with PHE 54 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431 PHE* 3.1 6.4 - - - +
441 LYS* 2.8 49.3 + - + +
461 GLN* 3.9 19.1 - - + -
521 ASN* 3.9 13.7 - - + -
531 TYR* 1.3 74.8 - - - +
551 ILE* 1.3 59.1 + - - +
671 LEU 3.1 7.6 - - - +
681 ARG* 3.6 30.1 - - + -
951 LEU* 3.4 13.3 - - + +
961 THR 4.3 4.0 - - - +
971 TYR* 3.3 38.8 - + + -
981 PHE* 3.4 56.8 - + - -
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Residues in contact with ILE 55 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161 THR* 3.8 28.5 - - + +
191 ILE* 3.7 35.9 - - + -
201 ALA* 4.2 8.7 - - + +
401 ALA* 3.9 7.2 - - + -
421 SER 3.5 11.0 - - - +
431 PHE* 4.2 2.2 - - + -
531 TYR* 4.1 17.5 - - + +
541 PHE* 1.3 79.6 - - - +
561 LYS* 1.3 65.8 + - - +
571 VAL* 3.6 20.3 + - + -
651 VAL 3.6 1.4 - - - +
661 HIS* 3.2 4.3 - - - -
671 LEU* 2.8 45.5 + - + +
691 VAL* 4.4 9.9 - - + -
951 LEU* 3.9 4.6 - - - +
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Residues in contact with LYS 56 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401 ALA* 3.7 2.3 - - - -
411 VAL* 2.8 48.9 + - + +
421 SER* 2.9 28.2 + - - +
551 ILE* 1.3 71.4 - - - +
571 VAL* 1.3 55.3 + - - +
641 PHE* 4.0 20.5 - - + +
651 VAL 3.7 2.9 - - - -
661 HIS* 3.0 33.5 + - + +
901 ALA 2.7 29.0 + - - -
911 LYS* 3.5 16.8 - - - +
931 ASP* 2.8 25.3 + - - +
951 LEU* 3.9 12.0 - - + +
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Residues in contact with VAL 57 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201 ALA* 4.3 5.6 - - + -
381 PHE* 3.7 30.1 - - + -
391 LYS 3.4 20.9 - - - +
401 ALA* 4.2 4.9 - - - +
551 ILE* 3.6 20.6 - - + +
561 LYS* 1.3 76.7 - - - +
581 HIS* 1.3 73.7 + - - +
591 VAL* 3.5 3.2 + - + +
641 PHE* 3.1 8.9 - - - -
651 VAL* 2.8 42.3 + - + +
671 LEU* 3.8 26.7 - - + -
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Residues in contact with HIS 58 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371 VAL* 3.5 15.7 - - + +
381 PHE* 3.4 6.1 + - - -
391 LYS* 2.8 59.7 + - + +
411 VAL* 4.3 6.9 - - + +
561 LYS 4.3 0.2 - - - -
571 VAL* 1.3 71.5 - - - +
591 VAL* 1.3 58.9 + - - +
601 GLY* 3.4 21.1 + - - -
611 ASP 3.6 1.9 + - - -
621 GLU* 3.2 31.4 - - - -
631 ASP 3.3 11.1 + - - -
641 PHE* 3.5 32.1 - + + -
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Residues in contact with VAL 59 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351 PHE* 3.7 19.3 - - + -
361 PRO* 3.1 23.9 - - - +
371 VAL* 3.1 13.5 - - - +
381 PHE* 3.7 31.0 - - + -
571 VAL* 3.9 7.0 - - + +
581 HIS* 1.3 77.6 - - - +
601 GLY* 1.3 56.8 + - - +
631 ASP* 3.0 32.7 + - + +
641 PHE 4.1 0.2 - - - +
651 VAL* 3.8 31.6 - - + -
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Residues in contact with GLY 60 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361 PRO* 4.7 7.0 - - - -
371 VAL* 3.2 19.1 - - - +
581 HIS* 3.4 8.1 - - - -
591 VAL* 1.3 77.4 - - - +
611 ASP* 1.3 72.0 + - - +
621 GLU 3.4 2.5 - - - -
631 ASP* 2.8 28.4 + - - +
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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