Contacts of the strand formed by residues 53 - 61 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17F ILE* 3.3 44.2 - - + -
18F HIS* 3.5 22.9 - - - -
19F PRO* 3.7 21.5 - - + -
34F VAL 3.7 0.3 - - - +
35F TYR* 3.4 4.9 - - - -
36F ALA 2.9 38.8 + - - +
38F PRO* 4.1 12.6 - - + -
51F PRO* 5.4 0.4 - - + -
52F LEU* 1.3 76.5 - - - +
54F THR* 1.3 59.8 + - - +
55F LEU* 3.8 18.2 - - + -
69F ILE* 4.1 15.9 - - + -
70F GLU 3.8 12.3 - - - +
71F HIS* 4.9 6.3 - + + -
138F GLY* 4.1 7.2 - - - -
139F TYR* 3.8 20.4 - - + -
150F MET* 4.2 7.4 - - + -
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Residues in contact with THR 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B GLN* 4.7 8.8 + - - +
353B LYS* 6.1 0.7 - - - -
33F VAL* 3.9 15.5 - - + -
34F VAL 3.8 2.0 - - - -
35F TYR* 3.8 31.0 - - + +
52F LEU* 4.4 5.9 + - - +
53F PHE* 1.3 74.0 - - - +
55F LEU* 1.3 63.3 + - - +
56F ARG* 3.9 9.3 + - + +
68F ARG 3.2 4.9 - - - +
70F GLU* 3.1 44.6 + - + +
73F GLN* 4.6 14.1 + - - +
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Residues in contact with LEU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F PRO* 4.5 4.3 - - + -
32F MET 3.7 1.4 - - - +
33F VAL* 3.4 2.5 - - - -
34F VAL* 2.7 52.6 + - + +
36F ALA* 4.1 13.7 - - + -
53F PHE* 3.8 28.5 - - + +
54F THR* 1.3 72.3 - - - +
56F ARG* 1.3 59.5 + - - +
57F PHE* 4.0 26.8 - - + -
67F VAL* 5.4 1.3 - - + -
68F ARG 3.5 4.0 - - - +
69F ILE* 4.1 31.4 - - + -
112F VAL* 5.2 0.4 - - + -
118F TRP* 3.9 26.5 - - + -
120F LEU* 5.0 7.0 - - + -
137F ASN* 5.1 2.2 - - - +
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Residues in contact with ARG 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F GLN* 2.9 32.9 + - - +
31F GLU* 2.6 43.1 + - + +
32F MET 3.5 7.4 - - - +
33F VAL* 3.6 22.8 - - + +
35F TYR* 5.9 0.2 + - - -
54F THR* 3.9 8.5 + - + +
55F LEU* 1.3 73.7 - - - +
57F PHE* 1.3 65.6 + - - +
58F PHE* 3.9 15.8 - - + -
66F GLY 3.6 1.2 - - - +
67F VAL* 3.6 5.4 - - - +
68F ARG* 3.0 52.4 + - + +
70F GLU* 5.9 1.0 + - - -
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Residues in contact with PHE 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F GLU* 3.4 5.2 - - - +
32F MET* 2.7 50.4 + - + +
34F VAL* 4.2 12.8 - - + -
55F LEU* 4.0 33.7 - - + -
56F ARG* 1.3 75.7 - - - +
58F PHE* 1.3 62.3 + - - +
65F VAL* 4.4 1.1 - - + -
66F GLY 3.4 3.4 - - - +
67F VAL* 3.7 33.7 - - + -
103F PHE* 3.7 26.9 - - + -
110F ALA* 3.6 29.4 - - + -
112F VAL* 3.8 30.5 - - + -
120F LEU* 4.5 11.0 - - + -
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Residues in contact with PHE 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ASN 4.6 0.2 - - - -
31F GLU* 3.4 29.6 - - + +
56F ARG* 3.9 20.0 - - + -
57F PHE* 1.3 78.6 - - - +
59F SER* 1.3 65.8 + - - +
60F PRO* 4.6 6.3 - - + -
65F VAL 3.6 0.2 - - - -
66F GLY* 2.8 44.6 + - - -
67F VAL 4.2 1.3 - - - -
68F ARG* 4.4 6.7 - - + -
86F ILE* 5.3 11.4 - - + -
103F PHE* 3.4 17.4 - - - -
238F GLU* 3.5 33.4 - - - -
240F PHE* 3.7 29.8 - + - -
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Residues in contact with SER 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ASN* 4.9 8.9 + - - +
58F PHE* 1.3 80.6 - - - +
60F PRO* 1.3 60.8 - - - +
61F GLN 2.9 9.7 + - - -
64F ILE 2.8 14.8 + - - -
86F ILE* 5.4 0.2 - - - +
87F LEU 3.9 5.7 - - - +
90F VAL* 3.4 18.6 + - - +
92F VAL* 3.7 21.7 - - - +
103F PHE* 3.5 8.2 - - - -
105F SER* 2.8 27.1 + - - -
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Residues in contact with PRO 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F PHE* 4.1 5.6 - - + +
59F SER* 1.3 84.9 - - - +
61F GLN* 1.3 71.4 + - - +
64F ILE* 3.4 23.8 - - + +
85F ASN 3.9 0.7 - - - +
86F ILE* 3.9 28.0 - - + -
87F LEU* 3.1 24.2 + - - +
90F VAL* 3.7 2.9 - - - -
240F PHE* 3.6 31.2 - - + -
257F PHE* 3.6 28.7 - - + -
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Residues in contact with GLN 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F SER* 2.9 13.7 + - - -
60F PRO* 1.3 91.4 - - - +
62F GLU* 1.3 69.2 + - - +
64F ILE* 2.9 31.2 + - + +
85F ASN* 4.0 12.7 - - - +
87F LEU* 4.1 15.8 - - + +
90F VAL* 3.9 8.3 - - - -
253F ARG* 3.4 26.1 + - - +
256F ARG* 3.2 45.3 - - - +
257F PHE* 3.5 18.1 - - + +
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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