Contacts of the strand formed by residues 39 - 47 (chain 5) 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 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175 GLN* 3.5 7.6 - - - +
375 VAL* 4.2 14.8 - - + -
385 PHE* 1.3 73.9 - - - +
405 ALA* 1.3 77.2 + - - +
415 VAL* 3.3 19.3 + - + +
575 VAL* 3.4 2.6 - - - +
585 HIS* 2.8 43.2 + - + -
886 ASN* 4.7 11.7 + - - -
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Residues in contact with ALA 40 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125 ALA* 3.3 21.9 - - + +
165 THR* 4.0 12.1 - - + +
175 GLN* 2.9 40.6 + - + +
205 ALA* 4.5 4.7 - - + +
385 PHE 3.9 1.0 + - - -
395 LYS* 1.3 83.9 - - - +
415 VAL* 1.3 62.1 + - - +
555 ILE* 4.1 9.0 - - + -
565 LYS 3.7 5.8 - - - -
575 VAL* 4.3 7.0 - - - +
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Residues in contact with VAL 41 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115 PRO* 3.5 5.7 - - - +
125 ALA* 2.7 27.3 + - - +
395 LYS* 3.8 26.9 - - + +
405 ALA* 1.3 75.1 - - - +
425 SER* 1.3 64.0 - - - +
565 LYS* 2.9 47.9 + - + +
585 HIS* 4.4 13.5 - - + -
645 PHE* 4.4 12.8 - - + -
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Residues in contact with SER 42 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95 THR* 5.1 5.9 - - - -
105 GLN 3.1 21.1 - - - -
115 PRO* 4.1 1.6 - - - -
125 ALA* 3.5 4.2 - - - +
165 THR* 4.8 1.3 - - - -
415 VAL* 1.3 84.0 - - - +
435 PHE* 1.3 66.8 + - - +
555 ILE* 3.4 6.6 - - - +
565 LYS* 2.8 45.2 + - - +
955 LEU* 4.2 7.7 - - - +
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Residues in contact with PHE 43 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95 THR* 3.1 1.7 - - - -
105 GLN* 2.7 72.7 + - + -
115 PRO 3.6 17.7 - - - -
125 ALA* 4.2 0.2 - - - -
135 THR* 4.5 10.3 - - + -
155 GLU* 6.5 0.9 - - - -
165 THR* 3.2 40.2 - - + -
425 SER* 1.3 77.4 - - - +
445 LYS* 1.3 70.5 + - - +
455 SER* 4.0 14.4 - - - -
535 TYR* 4.5 16.6 - + + -
545 PHE 3.0 17.0 - - - +
555 ILE* 4.3 2.9 - - + -
955 LEU* 3.6 8.2 - - - +
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Residues in contact with LYS 44 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85 ALA* 4.1 15.0 - - - +
95 THR* 3.3 40.5 - - + +
105 GLN* 3.9 4.7 - - - +
435 PHE* 1.3 82.1 - - - +
455 SER* 1.3 62.4 + - - +
535 TYR 3.9 0.3 - - - -
545 PHE* 2.9 44.3 + - + +
945 GLU* 5.3 4.8 + - - +
955 LEU* 3.9 18.4 + - + +
965 THR* 5.6 0.4 - - - +
975 TYR* 3.8 46.8 - - + +
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Residues in contact with SER 45 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105 GLN* 4.8 1.6 - - - +
435 PHE* 4.0 9.3 - - - -
445 LYS* 1.3 77.8 - - - +
465 GLN* 1.3 64.2 + - - +
475 VAL* 6.0 1.8 - - - +
515 THR* 4.0 7.6 - - - +
525 ASN 3.1 9.2 - - - -
535 TYR* 3.6 29.9 - - - -
975 TYR* 4.1 9.2 + - - -
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Residues in contact with GLN 46 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455 SER* 1.3 74.0 - - - +
475 VAL* 1.3 64.0 + - - +
485 VAL* 3.5 12.5 + - - +
515 THR* 3.4 3.6 - - - -
525 ASN* 2.6 67.0 + - + +
545 PHE* 4.0 8.9 - - + -
685 ARG* 5.3 1.8 - - - +
975 TYR* 2.8 50.8 + - + +
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Residues in contact with VAL 47 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455 SER* 4.3 2.0 - - - +
465 GLN* 1.3 73.3 - - - +
485 VAL* 1.3 79.6 + - - +
505 GLY 4.0 7.4 - - - +
515 THR* 4.5 11.7 - - + +
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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
------------------------------------------------------------
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