Contacts of the strand formed by residues 108 - 113 (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 LEU 108 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F GLY* 3.5 15.7 - - - +
65F VAL* 3.8 20.0 - - + +
104F LYS* 3.4 1.1 - - - -
105F SER 2.8 36.3 + - - +
107F ASN* 1.3 79.2 - - - +
109F SER* 1.3 68.3 + - - +
122F PHE* 4.6 6.1 - - + -
123F LEU 3.3 17.7 - - - +
124F ARG* 4.7 0.4 - - - +
129F ILE* 3.7 28.5 - - + -
241F VAL* 3.3 36.3 - - + +
243F ASP* 3.8 26.2 + - + +
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Residues in contact with SER 109 (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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65F VAL* 4.6 4.5 - - - -
102F GLU* 2.9 28.9 + - - -
103F PHE 2.9 13.9 - - - -
104F LYS* 3.6 18.7 + - - +
107F ASN 4.0 0.4 + - - -
108F LEU* 1.3 78.7 - - - +
110F ALA* 1.3 60.8 + - - +
121F ASP 3.7 0.2 - - - +
122F PHE* 3.3 7.4 - - - +
123F LEU* 2.9 48.8 + - - +
126F GLY 5.4 1.6 + - - -
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Residues in contact with ALA 110 (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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32F MET* 5.4 0.2 - - - +
57F PHE* 3.6 38.1 - - + -
65F VAL* 3.9 17.2 - - + +
101F ALA 3.6 1.2 - - - +
102F GLU* 3.2 5.0 - - - +
103F PHE* 2.7 33.1 + - + +
109F SER* 1.3 74.5 - - - +
111F ARG* 1.3 59.0 + - - +
112F VAL* 5.6 0.7 - - - -
120F LEU* 4.8 0.7 - - + -
121F ASP 3.3 5.8 - - - +
122F PHE* 3.9 13.0 - - + -
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Residues in contact with ARG 111 (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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100F TYR* 3.6 61.7 + - + -
101F ALA 3.4 2.2 - - - +
102F GLU* 3.7 29.5 + - + -
109F SER 4.1 0.2 - - - -
110F ALA* 1.3 74.8 - - - +
112F VAL* 1.3 63.9 + - - +
113F SER* 4.1 1.8 + - - -
119F SER 3.4 4.3 - - - +
120F LEU* 3.4 1.3 - - - +
121F ASP* 2.7 65.9 + - + +
123F LEU* 3.8 30.4 - - + +
126F GLY* 5.5 3.0 + - - -
128F ARG* 6.2 0.2 - - - +
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Residues in contact with VAL 112 (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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22F VAL* 3.4 29.2 - - + -
34F VAL* 4.5 8.1 - - + -
57F PHE* 3.8 34.3 - - + -
100F TYR* 3.4 6.9 - - - -
101F ALA* 2.9 41.6 + - + +
111F ARG* 1.3 76.5 - - - +
113F SER* 1.3 64.8 + - - +
114F LYS* 3.6 1.6 + - - +
118F TRP* 3.7 24.9 - - + -
119F SER 3.2 6.1 - - - +
120F LEU* 4.3 11.9 - - + -
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Residues in contact with SER 113 (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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22F VAL* 3.9 10.0 + - - +
99F ARG 3.9 5.6 - - - -
100F TYR* 3.8 21.7 - - - -
111F ARG* 4.1 1.1 + - - -
112F VAL* 1.3 72.7 - - - +
114F LYS* 1.3 65.9 + - - +
115F GLY 4.7 0.5 - - - +
117F PHE 3.4 20.0 - - - -
118F TRP* 3.9 15.9 - - - -
119F SER* 3.0 28.4 + - - -
121F ASP* 4.6 4.7 + - - -
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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