Contacts of the strand formed by residues 100 - 105 (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 TYR 100 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95D GLU* 5.9 3.1 - - - +
96D ASN 3.8 0.3 - - - -
97D THR* 2.8 45.0 + - - +
98D GLU 3.7 0.6 - - - -
99D ARG* 1.3 143.0 + - + +
101D ALA* 1.3 58.3 + - - +
102D GLU* 5.5 1.3 - - + -
111D ARG* 3.8 51.7 + - + -
112D VAL 3.5 5.6 - - - +
113D SER* 3.1 35.7 - - - -
114D LYS* 3.8 5.2 - - - -
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Residues in contact with ALA 101 (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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25D VAL* 4.0 30.7 - - + -
32D MET* 4.0 17.3 - - - -
34D VAL* 5.0 2.5 - - + -
95D GLU 3.2 8.1 - - - +
96D ASN* 4.1 2.9 - - - +
100D TYR* 1.3 73.9 - - - +
102D GLU* 1.3 61.3 + - - +
110D ALA 3.9 0.2 - - - +
111D ARG* 3.3 4.1 - - - +
112D VAL* 2.9 42.8 + - + +
114D LYS* 4.3 2.5 - - + -
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Residues in contact with GLU 102 (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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32D MET* 2.8 22.9 - - - +
93D THR* 3.7 1.4 - - - +
94D ILE* 3.6 1.2 - - - -
95D GLU* 2.7 48.5 + - + +
100D TYR* 5.5 1.1 - - + -
101D ALA* 1.3 75.5 - - - +
103D PHE* 1.3 59.4 + - - +
104D LYS* 4.2 13.0 + - + +
109D SER* 2.9 31.4 + - - +
110D ALA 3.1 12.6 - - - +
111D ARG* 3.4 28.4 + - + -
123D LEU* 4.2 7.0 - - - +
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Residues in contact with PHE 103 (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 3.4 22.7 - - - -
32D MET* 3.6 16.6 - - + -
57D PHE* 3.9 24.2 - - + -
58D PHE* 3.5 37.0 - - - -
59D SER* 3.8 11.4 - - - -
65D VAL* 4.1 22.9 - - + -
92D VAL* 3.8 22.2 - - + -
93D THR 3.6 1.1 - - - -
94D ILE* 3.5 28.5 - - + -
102D GLU* 1.3 73.4 - - - +
104D LYS* 1.3 63.9 + - - +
109D SER* 2.8 4.5 - - - -
110D ALA* 2.5 44.8 + - + +
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Residues in contact with LYS 104 (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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92D VAL* 3.1 11.5 - - - +
93D THR* 2.9 50.5 + - + +
102D GLU* 4.4 10.3 + - + +
103D PHE* 1.3 78.8 - - - +
105D SER* 1.3 62.9 + - - +
106D GLY 3.5 20.9 - - - +
107D ASN* 4.2 16.2 - - - +
108D LEU 3.4 9.0 - - - +
109D SER* 3.5 13.9 + - - -
125D ASN* 4.5 20.3 - - - +
126D GLY 4.9 3.4 - - - +
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Residues in contact with SER 105 (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* 2.8 36.4 + - - -
61D GLN 3.4 1.9 + - - -
62D GLU* 3.7 4.5 - - - -
63D GLY* 3.4 19.3 + - - -
64D ILE 4.1 7.0 - - - -
65D VAL* 4.1 9.3 - - - +
90D VAL* 3.9 6.4 - - - +
91D LYS 4.4 3.0 + - - -
92D VAL* 4.0 5.8 - - - -
103D PHE* 4.7 0.2 - - - -
104D LYS* 1.3 74.5 - - - +
106D GLY* 1.3 65.2 + - - +
107D ASN 3.3 0.2 + - - -
108D LEU* 2.7 30.0 + - - +
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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