Contacts of the strand formed by residues 63 - 71 (chain D) in PDB entry 3ZJX
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 TYR 63 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61D ASP 3.9 7.6 - - - +
62D PHE* 1.3 77.0 - - - +
64D ILE* 1.3 84.4 + - - +
65D ASN* 3.3 27.5 + - - -
66D ASN 5.6 0.4 - - - -
125D ILE* 4.2 4.0 - - + +
126D GLN 6.1 1.8 - - - -
197D GLN 3.7 0.7 - - - +
198D VAL* 3.2 6.4 - - - +
199D SER* 3.0 40.5 + - - +
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Residues in contact with ILE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D TYR* 1.3 87.1 - - - +
65D ASN* 1.3 62.0 + - - +
67D PRO* 3.7 25.4 - - + +
121D VAL* 4.2 10.1 - - + -
125D ILE* 3.6 41.9 - - + +
126D GLN 4.7 1.6 + - - +
127D ALA* 3.7 30.5 - - + +
148D PHE* 4.3 6.7 - - + -
196D GLY* 4.2 18.8 - - - -
197D GLN 3.8 3.4 - - - +
198D VAL* 4.1 7.0 - - + -
238D ILE* 3.7 28.9 - - + -
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Residues in contact with ASN 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D TYR* 3.3 23.3 + - - -
64D ILE* 1.3 69.7 - - - +
66D ASN* 1.3 82.9 + - - +
67D PRO 3.4 0.3 - - - -
196D GLY* 3.6 1.2 - - - -
197D GLN* 2.7 54.3 + - + +
199D SER* 3.1 32.9 + - - +
235D THR* 4.0 9.2 - - + +
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Residues in contact with ASN 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D TYR* 5.6 0.6 - - - -
65D ASN* 1.3 81.7 - - - +
67D PRO* 1.3 74.2 - - - +
68D LYS* 3.4 30.1 + - - +
195D VAL* 3.8 5.7 - - - +
196D GLY* 4.0 3.3 - - - -
197D GLN* 3.7 19.1 + - - +
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Residues in contact with PRO 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D TYR* 6.2 0.4 - - + -
64D ILE* 3.7 20.4 - - + +
65D ASN 3.4 2.1 - - - +
66D ASN* 1.3 91.3 - - - +
68D LYS* 1.3 63.7 + - - +
127D ALA* 4.3 8.5 - - + -
128D THR 3.6 23.1 - - - +
129D ALA* 3.7 8.5 - - - +
148D PHE* 3.6 21.3 - - + -
195D VAL 3.4 8.5 - - - +
196D GLY* 4.5 1.3 - - - -
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Residues in contact with LYS 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D ASN* 3.6 26.8 + - - +
67D PRO* 1.3 79.7 - - - +
69D VAL* 1.3 69.6 + - - +
70D GLU* 5.1 10.1 - - + +
129D ALA* 3.7 6.7 - - - -
130D LYS 5.7 0.2 - - - -
148D PHE* 3.9 1.8 - - - -
194D LEU* 3.6 3.3 - - - -
195D VAL* 2.9 44.1 + - + +
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Residues in contact with VAL 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LYS* 1.3 76.5 - - - +
70D GLU* 1.3 68.0 + - - +
129D ALA* 3.6 24.2 - - + +
130D LYS 3.5 25.6 + - - +
131D PHE* 3.9 17.6 - - + -
146D TYR* 3.9 17.0 - - + -
192D VAL* 3.6 37.9 - - + -
193D LYS 3.6 2.5 - - - -
194D LEU* 4.0 10.5 - - + -
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Residues in contact with GLU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LYS* 5.1 10.2 - - + +
69D VAL* 1.3 79.6 - - - +
71D LEU* 1.3 61.4 + - - +
131D PHE* 6.1 0.2 - - - -
192D VAL* 3.1 7.6 - - - -
193D LYS* 2.7 74.5 + - + +
195D VAL* 3.7 27.4 - - + +
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Residues in contact with LEU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D GLU* 1.3 74.2 - - - +
72D ASP* 1.3 58.5 + - - +
73D GLY 3.8 12.5 + - - +
74D GLU* 5.1 7.2 - - - +
75D PRO* 4.6 13.7 - - + -
131D PHE* 3.9 27.8 - - + -
132D THR 5.6 0.2 - - - +
134D PRO* 4.0 23.8 - - + -
135D PHE* 6.0 1.3 - - + -
191D ASN 3.9 3.4 - - - +
192D VAL* 4.4 0.9 - - + +
193D LYS* 3.6 13.7 + - - -
244D TYR* 4.0 21.5 - - + +
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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