Contacts of the strand formed by residues 64 - 70 (chain D) in PDB entry 1XSK
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 ILE 64 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59D SER* 2.7 32.4 + - - -
60D PRO* 3.7 19.7 - - + -
61D GLN* 3.0 22.9 + - + +
63D GLY* 1.3 84.6 - - - +
65D VAL* 1.3 65.0 + - - +
105D SER* 4.1 0.6 + - - -
240D PHE* 3.8 23.6 - - + -
241D VAL 3.4 8.7 - - - +
242D ILE* 4.1 24.7 - - + -
253D ARG* 4.1 15.7 - - + +
257D PHE* 3.6 40.2 - - + -
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Residues in contact with VAL 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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57D PHE* 4.5 0.9 - - + -
58D PHE 3.7 2.5 - - - -
64D ILE* 1.3 76.2 - - - +
66D GLY* 1.3 70.8 - - - +
67D VAL* 3.8 10.0 + - + +
103D PHE* 4.1 21.1 - - + -
105D SER* 4.1 11.9 - - - -
108D LEU* 3.9 41.0 - - + +
109D SER* 4.6 3.4 - - - -
110D ALA* 3.9 24.7 - - + -
122D PHE* 4.7 3.6 - - + -
239D TYR 4.0 0.2 - - - +
240D PHE* 3.6 2.7 - - - -
241D VAL* 2.9 36.3 + - + +
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Residues in contact with GLY 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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57D PHE* 3.3 7.4 - - - -
58D PHE* 2.7 46.5 + - - +
60D PRO* 4.3 0.2 - - - +
64D ILE 3.9 1.2 + - - -
65D VAL* 1.3 73.9 - - - +
67D VAL* 1.3 62.2 + - - +
239D TYR 3.6 0.4 - - - -
240D PHE* 3.3 33.4 - - - -
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Residues in contact with VAL 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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55D LEU* 5.2 4.9 - - + -
56D ARG 3.6 3.6 - - - +
57D PHE* 3.9 28.5 - - + -
58D PHE* 4.0 2.4 - - - -
65D VAL* 4.1 7.9 - - + +
66D GLY* 1.3 79.2 - - - +
68D ARG* 1.3 67.3 + - - +
69D ILE* 4.7 6.3 - - + -
120D LEU* 5.0 5.4 - - + -
122D PHE* 3.8 31.9 - - + -
237D LEU 3.7 1.2 - - - +
238D GLU* 3.1 4.6 - - - +
239D TYR* 2.8 68.0 + - + +
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Residues in contact with ARG 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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54D THR 3.4 3.1 - - - +
55D LEU* 3.3 2.2 - - - -
56D ARG* 2.8 57.6 + - + +
58D PHE* 4.3 7.9 - - + -
67D VAL* 1.3 75.3 - - - +
69D ILE* 1.3 63.9 + - - +
70D GLU* 3.7 30.0 + - - +
77D ASN* 5.0 4.8 + - - +
236D TYR* 3.7 46.7 + - + -
237D LEU 3.5 2.9 - - - -
238D GLU* 2.8 43.4 + - + +
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Residues in contact with ILE 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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19D PRO* 4.6 13.5 - - + -
53D PHE* 4.0 20.2 - - + -
54D THR 3.6 3.4 - - - -
55D LEU* 4.0 22.2 - - + +
67D VAL* 4.7 11.4 - - + -
68D ARG* 1.3 75.2 - - - +
70D GLU* 1.3 62.2 + - - +
137D ASN* 4.7 12.1 - - + +
138D GLY* 4.4 15.0 - - - +
150D MET* 3.3 24.1 - - + +
151D PHE 5.4 0.4 - - - +
152D GLU* 5.8 0.9 - - + +
236D TYR* 3.3 2.2 - - - -
237D LEU* 2.9 56.4 + - + +
239D TYR* 4.8 7.2 - - + -
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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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52D LEU 4.4 0.2 - - - +
53D PHE* 3.7 11.4 - - - -
54D THR* 3.1 46.0 + - - +
56D ARG* 5.5 5.9 + - - +
68D ARG* 3.7 34.8 + - + +
69D ILE* 1.3 76.1 - - - +
71D HIS* 1.3 64.4 + - - +
72D PHE 4.8 1.6 - - - +
73D GLN* 3.1 47.9 + - + +
150D MET* 4.6 0.9 - - - -
235D GLU 3.6 3.8 - - - +
236D TYR* 3.4 17.8 - - + +
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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