Contacts of the strand formed by residues 53 - 61 (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 PHE 53 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ILE* 3.3 43.5 - - + -
18D HIS* 3.4 24.2 - - - -
19D PRO* 3.7 19.7 - - + -
34D VAL 3.7 0.7 - - - +
35D TYR* 3.5 1.7 - - - -
36D ALA 2.9 38.5 + - - +
38D PRO* 4.3 10.1 - - + -
51D PRO* 5.5 0.7 - - + -
52D LEU* 1.3 79.1 - - - +
54D THR* 1.3 60.7 + - - +
55D LEU* 4.0 16.6 - - + -
69D ILE* 4.0 19.5 - - + -
70D GLU 3.7 10.8 - - - +
71D HIS* 4.9 7.2 - + - +
138D GLY* 3.9 10.3 - - - -
139D TYR* 3.8 21.5 - - + -
150D MET* 4.3 6.7 - - + -
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Residues in contact with THR 54 (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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352C GLN* 4.7 9.2 + - - -
353C LYS* 5.9 1.0 - - - -
33D VAL* 3.9 23.8 - - + -
34D VAL 3.7 2.9 - - - -
35D TYR* 3.7 21.1 - - + -
52D LEU* 4.2 5.5 + - - +
53D PHE* 1.3 73.7 - - - +
55D LEU* 1.3 61.2 + - - +
56D ARG* 5.3 7.8 - - + +
68D ARG 3.4 4.7 - - - +
70D GLU* 3.1 53.3 + - - +
73D GLN* 4.5 9.4 + - - +
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Residues in contact with LEU 55 (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 4.0 - - + -
32D MET 3.7 0.5 - - - +
33D VAL* 3.3 5.9 - - - +
34D VAL* 2.7 53.7 + - + +
36D ALA* 4.0 23.6 - - + -
53D PHE* 4.0 13.9 - - + -
54D THR* 1.3 75.9 - - - +
56D ARG* 1.3 60.5 + - - +
57D PHE* 3.9 29.3 - - + -
67D VAL* 5.2 4.5 - - + -
68D ARG 3.3 5.2 - - - +
69D ILE* 4.0 24.0 - - + -
112D VAL* 5.4 0.2 - - + -
118D TRP* 4.1 24.7 - - + -
120D LEU* 4.7 9.9 - - + -
137D ASN* 5.4 2.2 - - - +
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Residues in contact with ARG 56 (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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28D GLN* 2.8 33.5 + - - +
31D GLU* 2.8 44.6 + - + +
32D MET 3.5 6.1 - - - +
33D VAL* 3.4 22.9 - - + +
54D THR* 5.3 6.8 - - + +
55D LEU* 1.3 74.3 - - - +
57D PHE* 1.3 68.5 + - - +
58D PHE* 3.8 13.5 - - + -
66D GLY 3.7 0.7 - - - +
67D VAL* 3.6 2.9 - - - -
68D ARG* 2.8 52.6 + - + +
70D GLU* 5.5 5.9 + - - +
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Residues in contact with PHE 57 (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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31D GLU* 3.4 6.4 - - - +
32D MET* 2.8 47.5 + - + +
34D VAL* 3.8 25.6 - - + -
55D LEU* 3.9 27.1 - - + -
56D ARG* 1.3 76.1 - - - +
58D PHE* 1.3 63.2 + - - +
65D VAL* 4.5 1.1 - - + -
66D GLY 3.3 5.8 - - - +
67D VAL* 3.9 31.9 - - + -
103D PHE* 3.9 26.5 - - + -
110D ALA* 3.5 32.5 - - + -
112D VAL* 3.8 20.9 - - + -
120D LEU* 4.6 11.2 - - + -
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Residues in contact with PHE 58 (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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30D ASN 4.7 0.2 - - - -
31D GLU* 3.5 31.6 - - + +
56D ARG* 3.8 19.7 - - + -
57D PHE* 1.3 78.1 - - - +
59D SER* 1.3 60.8 + - - +
60D PRO* 4.6 9.6 - - + -
65D VAL 3.6 0.3 - - - -
66D GLY 2.7 48.4 + - - +
67D VAL 4.0 1.3 - - - -
68D ARG* 4.3 12.8 - - + -
86D ILE* 5.8 10.3 - - + -
88D GLN* 6.3 0.9 - - - -
103D PHE* 3.5 16.3 - - - -
238D GLU* 3.8 19.7 - - - -
240D PHE* 3.7 32.1 - + - -
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Residues in contact with SER 59 (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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30D ASN* 5.2 7.8 + - - +
58D PHE* 1.3 82.3 - - - +
60D PRO* 1.3 64.0 - - - +
61D GLN 2.7 28.8 + - - -
64D ILE 2.7 10.6 + - - -
87D LEU 3.9 6.3 - - - +
90D VAL* 3.7 15.5 - - - +
92D VAL* 3.8 16.9 - - - +
103D PHE* 3.8 4.2 - - - -
105D SER* 2.8 23.8 + - - -
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Residues in contact with PRO 60 (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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58D PHE* 4.1 7.8 - - + +
59D SER* 1.3 86.3 - - - +
61D GLN* 1.3 67.5 + - - +
64D ILE* 3.6 26.9 - - + +
85D ASN 4.2 0.7 - - - +
86D ILE* 4.1 20.4 - - + -
87D LEU* 3.2 38.7 + - - +
90D VAL* 3.9 1.6 - - - -
240D PHE* 3.8 17.9 - - + -
257D PHE* 3.5 38.1 - - + -
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Residues in contact with GLN 61 (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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59D SER* 2.7 23.8 + - - -
60D PRO* 1.3 86.8 + - - +
62D GLU* 1.3 67.4 + - - +
63D GLY 3.2 0.2 + - - -
64D ILE* 3.0 28.1 + - + -
85D ASN* 2.9 36.4 + - - +
87D LEU* 3.4 24.6 - - - +
90D VAL* 4.1 7.6 - - - -
253D ARG* 5.4 1.3 - - + +
256D ARG* 3.5 33.4 + - - +
257D PHE* 4.0 23.8 - - + +
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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