Contacts of the strand formed by residues 90 - 98 (chain F) in PDB entry 5TSW
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 LYS 90 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47F GLN* 6.0 0.2 - - - +
81F SER* 2.9 33.4 + - - +
82F ARG 3.6 8.5 - - - +
83F ILE* 4.2 18.2 - - + +
88F GLN 3.2 4.3 + - - +
89F THR* 1.3 84.2 - - - +
91F VAL* 1.3 60.1 + - - +
92F ASN* 4.4 7.0 + - - +
133F SER* 4.9 2.9 - - - +
135F GLU* 3.5 29.7 + - - +
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Residues in contact with VAL 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ALA* 5.4 4.0 - - + -
34D ASN* 3.7 28.9 - - - +
147D SER* 5.5 6.1 - - - +
81F SER* 3.2 4.2 - - - -
82F ARG* 2.8 56.4 + - + +
89F THR* 4.5 5.8 - - + +
90F LYS* 1.3 76.9 - - - +
92F ASN* 1.3 72.2 + - - +
93F LEU* 3.7 3.5 + - + -
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Residues in contact with ASN 92 (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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34D ASN* 5.0 1.9 + - - +
147D SER* 3.9 34.6 + - - +
148D GLY 4.1 2.8 + - - -
79F THR* 4.3 18.2 + - - +
80F ILE 3.9 3.4 - - - -
81F SER* 3.6 17.2 - - - -
90F LYS* 4.4 9.0 + - - +
91F VAL* 1.3 82.3 - - - +
93F LEU* 1.3 62.9 + - - +
94F LEU 3.5 7.4 - - - +
95F SER* 4.3 13.1 + - - -
135F GLU* 4.7 0.5 - - - +
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Residues in contact with LEU 93 (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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15D HIS* 4.9 2.1 + - - -
34D ASN* 3.3 43.2 - - + +
148D GLY* 3.6 11.8 - - - -
151D TYR* 5.0 0.7 - - - -
58F ILE* 4.3 9.0 - - + -
80F ILE* 3.0 15.9 + - + +
81F SER 4.8 0.9 - - - +
82F ARG* 3.7 34.8 - - + +
91F VAL* 3.7 3.8 + - + -
92F ASN* 1.3 74.0 - - - +
94F LEU* 1.3 66.3 + - + +
124F PHE* 3.4 46.7 - - + -
126F LEU* 4.3 6.5 - - + -
132F LEU* 4.0 18.2 - - + -
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Residues in contact with LEU 94 (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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148D GLY* 3.6 6.1 - - - -
151D TYR* 3.5 33.2 - - + -
58F ILE* 3.9 11.7 - - + +
79F THR* 3.6 3.6 - - - -
80F ILE* 3.1 53.8 + - + +
92F ASN* 4.5 1.0 - - - +
93F LEU* 1.3 81.3 + - + +
95F SER* 1.3 63.9 + - - +
120F LEU* 3.6 15.7 - - + -
121F GLY* 3.7 20.0 - - - +
122F GLY 3.7 13.5 - - - +
124F PHE* 3.4 31.4 - - + -
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Residues in contact with SER 95 (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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61D GLN* 2.7 28.0 + - - +
63D LEU* 4.9 0.2 - - - +
147D SER 3.5 21.9 + - - -
148D GLY 3.0 10.6 + - - +
149D GLN* 3.6 19.5 + - - +
78F HIS 3.8 5.8 - - - -
79F THR* 3.2 19.7 - - - +
92F ASN* 4.3 8.7 + - - -
94F LEU* 1.3 77.2 - - - +
96F ALA* 1.3 57.0 + - - +
97F ILE* 5.0 4.7 - - - +
120F LEU* 3.7 3.4 - - - +
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Residues in contact with ALA 96 (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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61D GLN* 4.2 9.2 - - - +
63D LEU* 4.8 4.3 - - - -
117D PRO* 4.3 15.9 - - + -
76F LEU 4.0 0.2 - - - +
77F THR* 3.5 2.1 - - - -
78F HIS 3.0 32.1 + - - +
79F THR* 4.9 0.2 - - - +
95F SER* 1.3 76.5 + - - +
97F ILE* 1.3 66.9 + - - +
118F ILE* 3.7 15.8 - - + +
119F TYR 5.5 0.2 - - - +
120F LEU* 3.4 26.0 - - + -
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Residues in contact with ILE 97 (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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63D LEU* 3.4 22.1 - - + +
115D TYR* 3.3 58.2 - - + +
117D PRO* 3.4 9.4 - - - +
143D ASP* 4.8 1.1 - - - +
149D GLN* 4.0 20.4 - - - +
75F LEU* 4.6 8.1 - - + -
76F LEU 3.3 11.0 - - - +
77F THR* 4.3 18.8 - - + -
95F SER* 5.0 4.9 - - - +
96F ALA* 1.3 82.4 - - - +
98F LYS* 1.3 67.9 + - - +
118F ILE* 4.9 1.3 - - - -
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Residues in contact with LYS 98 (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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98D LYS* 4.0 18.6 - - - +
115D TYR* 3.5 14.8 - - - +
116D GLU* 4.5 5.3 + - - +
117D PRO* 3.7 24.0 - - + -
98E LYS* 3.8 22.6 - - - +
75F LEU* 3.4 7.6 - - - +
76F LEU* 2.8 41.6 + - + +
97F ILE* 1.3 70.9 - - - +
99F SER* 1.3 62.3 + - - +
100F PRO* 4.2 0.9 - - - -
116F GLU* 2.7 45.5 + - + +
117F PRO 3.3 24.9 + - - -
118F ILE* 4.1 15.0 - - + -
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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