Contacts of the strand formed by residues 100 - 105 (chain C) 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 TYR 100 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C GLU* 4.0 2.4 - - + +
96C ASN* 3.9 0.2 - - - -
97C THR* 2.9 40.5 + - - +
99C ARG* 1.3 143.2 + - + +
101C ALA* 1.3 62.4 + - - +
102C GLU* 4.2 4.3 - - + +
111C ARG* 3.5 52.6 + - + -
112C VAL 3.4 6.5 - - - +
113C SER* 3.3 29.8 - - - -
114C LYS* 4.4 3.8 - - - +
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Residues in contact with ALA 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C VAL* 6.2 0.2 - - + -
25C VAL* 4.0 19.7 - - + -
32C MET* 3.9 19.2 - - + +
34C VAL* 4.6 2.9 - - + -
95C GLU 3.6 5.4 - - - -
96C ASN* 3.9 15.7 - - - +
100C TYR* 1.3 74.0 - - - +
102C GLU* 1.3 60.0 + - - +
110C ALA 3.8 1.0 - - - +
111C ARG* 3.5 2.1 - - - +
112C VAL* 2.9 44.7 + - + +
114C LYS* 4.4 2.9 - - + -
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Residues in contact with GLU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C MET* 2.9 17.8 - - - +
93C THR* 3.7 3.2 - - + +
94C ILE* 3.5 2.3 - - - -
95C GLU* 2.9 54.0 + - + +
100C TYR* 4.2 3.9 - - + +
101C ALA* 1.3 75.3 - - - +
103C PHE* 1.3 59.5 + - - +
104C LYS* 4.6 10.3 + - + +
109C SER* 3.2 28.4 + - - +
110C ALA 3.4 13.2 - - - +
111C ARG* 3.5 31.3 + - + -
123C LEU* 5.4 1.5 - - - +
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Residues in contact with PHE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ASN 2.9 28.9 - - - -
32C MET* 3.5 11.7 - - + +
57C PHE* 3.9 36.3 - - + -
58C PHE 3.4 35.4 - - - -
59C SER* 3.6 9.4 - - - -
65C VAL* 4.2 18.8 - - + -
92C VAL* 3.5 29.8 - - + -
93C THR 3.6 1.8 - - - -
94C ILE* 3.6 19.5 - - + -
102C GLU* 1.3 72.4 - - - +
104C LYS* 1.3 62.6 + - - +
105C SER* 4.6 2.5 - - - -
109C SER* 3.1 5.1 - - - -
110C ALA* 2.9 35.5 + - + +
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Residues in contact with LYS 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LYS 4.3 0.2 - - - +
92C VAL* 3.2 9.4 - - - +
93C THR* 2.8 60.5 + - + -
102C GLU* 4.6 8.7 + - - +
103C PHE* 1.3 80.4 - - - +
105C SER* 1.3 63.4 + - - +
106C GLY 3.1 24.7 - - - +
107C ASN* 3.8 21.1 + - - +
108C LEU 3.4 9.6 - - - +
109C SER* 3.7 12.8 - - - -
125C ASN* 4.4 15.4 + - - +
126C GLY 5.0 2.8 - - - +
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Residues in contact with SER 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C SER* 2.6 36.5 + - - -
62C GLU* 3.5 7.4 - - - -
63C GLY* 3.3 24.6 + - - -
64C ILE 4.2 5.4 - - - -
65C VAL* 4.4 7.8 - - - +
90C VAL* 3.9 6.6 - - - +
91C LYS 4.3 5.7 + - - -
92C VAL* 4.5 1.1 - - - -
103C PHE* 4.6 0.7 - - - -
104C LYS* 1.3 73.7 - - - +
106C GLY* 1.3 65.3 + - - +
107C ASN 3.2 0.2 + - - -
108C LEU* 2.8 25.6 + - - +
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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