Contacts of the strand formed by residues 81 - 89 (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 81 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231 VAL* 4.3 0.4 - - - -
261 GLN* 3.6 5.8 - - - -
691 VAL* 3.4 5.5 - - - +
701 PHE* 2.8 59.1 + - + +
781 LYS* 5.4 4.5 - - + -
791 PRO* 2.8 22.2 - - + +
801 LEU* 1.3 73.8 - - - +
821 LEU* 1.3 60.9 + - - +
831 SER* 3.2 7.8 + - - -
346 LYS* 4.0 23.1 - - + +
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Residues in contact with LEU 82 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231 VAL* 4.1 12.9 - - + +
261 GLN* 2.8 31.9 + - + +
271 LEU* 3.7 38.8 - - + +
301 LYS* 5.3 2.5 - - + -
671 LEU* 3.8 29.2 - - + -
681 ARG 3.5 7.6 - - - +
691 VAL* 4.1 6.3 - - + +
811 THR* 1.3 71.5 - - - +
831 SER* 1.3 60.1 + - - +
841 ASN* 3.3 24.9 - - - +
851 TYR* 3.9 19.5 - - + -
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Residues in contact with SER 83 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521 ASN* 4.9 0.7 + - - -
681 ARG* 2.7 36.4 + - - -
691 VAL 4.4 0.3 - - - -
701 PHE* 3.5 29.3 + - - +
811 THR* 3.2 4.7 + - - -
821 LEU* 1.3 74.3 - - - +
841 ASN* 1.3 62.1 + - - +
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Residues in contact with ASN 84 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681 ARG* 2.9 32.7 + - + -
821 LEU* 3.3 8.2 - - - +
831 SER* 1.3 81.4 - - - +
851 TYR* 1.3 81.5 + - - +
981 PHE* 3.8 35.3 + - + -
882 ASN* 3.1 20.6 + - - +
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Residues in contact with TYR 85 (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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271 LEU* 3.5 29.4 - - + -
301 LYS* 3.3 51.2 + - + +
311 GLU* 2.7 28.9 + - - -
651 VAL* 4.4 1.6 - - + -
661 HIS 3.1 14.4 - - - +
671 LEU* 4.3 10.1 - - + -
821 LEU* 3.9 11.7 - - + -
841 ASN* 1.3 87.4 + - - +
861 GLN* 1.3 70.3 + - - +
871 THR* 3.8 18.2 - - + -
981 PHE* 3.7 3.4 - - - -
872 THR 5.5 0.3 - - - +
882 ASN* 3.1 48.6 + - + +
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Residues in contact with GLN 86 (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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651 VAL* 3.4 4.5 - - - +
661 HIS* 2.8 42.1 + - + +
851 TYR* 1.3 79.9 - - - +
871 THR* 1.3 64.9 + - - +
891 LYS* 3.0 36.9 + - - +
961 THR* 4.3 8.5 + - - -
981 PHE* 3.3 49.6 - - + +
862 GLN* 6.1 0.6 - - - +
872 THR 6.0 1.8 - - - -
882 ASN* 5.9 1.1 - - - -
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Residues in contact with THR 87 (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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271 LEU* 5.1 0.2 - - + -
311 GLU* 3.8 25.7 + - + +
351 PHE* 6.0 1.3 - - + -
641 PHE 4.2 4.9 - - - -
651 VAL* 4.2 17.7 - - + -
851 TYR* 3.8 25.1 - - + -
861 GLN* 1.3 76.9 - - - +
881 ASN* 1.3 78.9 + - - +
891 LYS* 3.2 11.9 + - - +
312 GLU* 4.5 6.8 + - - -
862 GLN* 6.0 1.2 - - - -
872 THR* 2.9 30.3 + - - +
882 ASN* 6.1 0.4 - - - +
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Residues in contact with ASN 88 (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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631 ASP* 6.0 2.5 - - - -
641 PHE 3.7 4.8 + - - -
651 VAL* 5.4 0.2 - - - +
871 THR* 1.3 82.2 - - - +
891 LYS* 1.3 64.5 + - - +
931 ASP* 4.4 2.3 - - - +
302 LYS* 2.9 25.9 + - - +
312 GLU* 5.0 1.3 + - - +
842 ASN* 3.1 19.2 + - - +
852 TYR* 3.1 68.4 + - + +
862 GLN* 5.8 1.1 - - - -
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Residues in contact with LYS 89 (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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621 GLU 4.0 0.9 - - - +
631 ASP* 3.8 4.7 - - - +
641 PHE* 2.9 36.8 + - + +
661 HIS* 3.7 45.2 + - + +
861 GLN* 3.0 44.6 + - - +
871 THR 3.6 9.4 - - - +
881 ASN* 1.3 85.5 - - - +
901 ALA* 1.3 61.9 + - - +
931 ASP* 3.4 14.6 + - + +
941 GLU 5.2 3.2 + - - -
961 THR* 5.0 5.9 + - - +
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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