Contacts of the strand formed by residues 100 - 105 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95E GLU 3.9 1.3 - - - +
97E THR* 2.8 49.1 + - + +
99E ARG* 1.3 144.1 + - + +
101E ALA* 1.3 60.9 + - - +
102E GLU* 4.3 1.8 - - + -
111E ARG* 3.5 51.5 + - + -
112E VAL 3.4 6.5 - - - +
113E SER* 3.3 36.7 + - - -
114E LYS* 3.7 5.5 - - - -
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Residues in contact with ALA 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E VAL* 3.7 29.4 - - + -
32E MET* 3.6 26.3 - - + +
34E VAL* 4.6 2.0 - - + -
95E GLU 3.7 2.9 - - - -
96E ASN* 4.1 1.8 - - - +
100E TYR* 1.3 75.6 - - - +
102E GLU* 1.3 61.7 + - - +
110E ALA 3.8 0.3 - - - +
111E ARG* 3.3 2.9 - - - +
112E VAL* 2.8 44.0 + - + +
114E LYS* 4.5 1.6 - - + -
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Residues in contact with GLU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E MET* 3.2 8.2 - - - +
93E THR 3.5 1.4 - - - +
94E ILE* 3.3 5.4 - - - -
95E GLU* 3.1 59.6 + - + +
100E TYR* 5.5 1.6 - - + -
101E ALA* 1.3 75.7 - - - +
103E PHE* 1.3 64.5 + - - +
104E LYS* 4.5 11.9 - - + +
109E SER* 3.5 29.0 + - - -
110E ALA 3.2 11.2 - - - +
111E ARG* 3.5 29.3 + - + +
123E LEU* 4.4 2.8 - - - +
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Residues in contact with PHE 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ASN 3.3 22.4 - - - -
32E MET* 4.0 10.3 - - + -
57E PHE* 3.6 37.0 - - + -
58E PHE* 3.5 34.3 - - - -
59E SER* 3.6 13.2 - - - -
65E VAL* 4.0 19.5 - - + -
92E VAL* 3.7 28.5 - - + -
93E THR 3.4 2.0 - - - -
94E ILE* 3.6 20.9 - - + -
102E GLU* 1.3 74.2 - - - +
104E LYS* 1.3 63.8 - - - +
105E SER* 4.6 2.0 - - - -
109E SER* 3.0 2.9 - - - -
110E ALA* 2.7 39.7 + - + +
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Residues in contact with LYS 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E VAL* 3.2 9.6 - - - +
93E THR* 2.8 53.1 + - + +
95E GLU* 6.1 0.2 - - - +
102E GLU* 4.5 11.9 - - + +
103E PHE* 1.3 79.6 - - - +
105E SER* 1.3 62.5 + - - +
106E GLY 3.1 25.0 + - - +
107E ASN* 3.9 18.8 + - - +
108E LEU 3.3 11.0 - - - +
109E SER* 3.6 13.0 - - - -
125E ASN* 4.9 14.5 - - - +
126E GLY 5.4 2.0 - - - +
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Residues in contact with SER 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E SER* 2.8 36.1 + - - -
62E GLU* 3.5 7.3 - - - -
63E GLY* 3.2 28.5 + - - -
64E ILE 4.1 6.1 - - - -
65E VAL* 4.5 7.5 - - - +
90E VAL* 3.7 5.5 - - - +
91E LYS 4.5 5.3 + - - -
92E VAL* 4.3 2.7 - - - -
103E PHE* 4.6 0.2 - - - -
104E LYS* 1.3 73.9 - - - +
106E GLY* 1.3 63.8 + - - +
107E ASN 3.3 0.3 + - - -
108E LEU* 2.8 22.2 + - - +
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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