Contacts of the strand formed by residues 91 - 98 (chain F) in PDB entry 5FHK
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 GLY 91 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A ASP* 3.4 14.6 - - - -
136A THR* 4.1 9.2 - - - -
90F SER* 1.3 80.3 + - - +
92F LYS* 1.3 60.8 + - - -
119F GLU 3.3 5.8 + - - -
120F ILE* 3.2 8.3 - - - +
121F ASN* 2.8 30.4 + - - -
277F LYS* 4.1 5.8 - - - -
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Residues in contact with LYS 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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132A GLN* 2.6 31.5 + - - +
133A LEU* 4.4 0.8 - - - +
134A ASP* 2.9 31.9 + - + +
137A GLU* 4.1 17.1 + - - +
212C ARG* 4.2 17.5 - - - +
91F GLY* 1.3 74.3 - - - -
93F ILE* 1.3 73.3 + - - +
94F LYS* 5.0 8.9 - - + +
121F ASN* 3.4 11.7 - - + +
123F GLU* 3.0 33.9 + - + +
139F ASP* 4.0 4.8 - - - +
277F LYS* 2.6 28.9 + - - +
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Residues in contact with ILE 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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92F LYS* 1.3 80.3 - - - +
94F LYS* 1.3 62.3 - - - +
95F ILE* 3.7 22.5 + - + -
113F PHE* 4.4 2.9 - - + -
120F ILE* 3.9 22.0 - - + -
121F ASN 2.7 12.6 + - - +
122F ILE* 3.5 10.3 - - + +
123F GLU 3.0 22.3 + - - +
139F ASP* 3.6 15.7 - - + -
140F VAL* 4.8 6.7 - - + -
277F LYS* 3.1 44.2 - - + +
278F VAL* 4.0 5.4 - - + -
281F PHE* 3.8 23.3 - - + -
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Residues in contact with LYS 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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92F LYS* 4.2 9.3 - - + +
93F ILE* 1.3 70.7 - - - +
95F ILE* 1.3 61.7 + - - +
123F GLU* 3.5 41.1 - - - +
125F THR* 5.2 1.3 - - - +
137F GLU* 3.1 41.0 + - - +
138F TRP* 3.8 28.6 - - + -
139F ASP* 2.8 47.1 + - - +
140F VAL 3.4 4.7 + - - +
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Residues in contact with ILE 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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93F ILE* 3.7 22.9 - - + +
94F LYS* 1.3 80.8 - - - +
96F SER* 1.3 61.2 + - - +
97F THR* 4.3 4.3 - - + -
110F LEU* 3.8 40.2 - - + -
122F ILE* 3.9 19.5 - - + -
123F GLU 3.0 9.1 + - - +
124F LEU* 3.4 13.9 - - + -
125F THR 3.0 22.7 + - - -
138F TRP* 3.4 8.5 - - - -
140F VAL* 3.2 25.8 - - + +
142F PHE* 4.3 14.6 - - + -
281F PHE* 4.4 8.7 - - + -
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Residues in contact with SER 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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95F ILE* 1.3 72.9 - - - +
97F THR* 1.3 66.6 + - - +
125F THR 3.3 9.9 + - - -
127F GLU* 4.1 12.0 + - - +
130F ALA* 5.6 0.9 - - - +
133F LEU* 3.4 29.0 - - - +
138F TRP* 3.7 23.4 - - - -
140F VAL 3.2 7.6 + - - -
141F ILE* 4.4 6.2 - - - +
142F PHE* 2.7 34.4 + - - +
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Residues in contact with THR 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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95F ILE* 4.3 5.6 - - + -
96F SER* 1.3 82.8 + - - +
98F PRO* 1.3 71.4 - - - +
102F THR* 2.7 23.8 + - - +
106F MET* 4.0 17.3 - - + -
124F LEU* 3.5 37.6 - - + +
125F THR 3.1 3.2 + - - -
126F THR* 3.2 4.7 - - - +
127F GLU* 2.8 25.7 + - - +
142F PHE* 3.5 23.3 - - + -
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Residues in contact with PRO 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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97F THR* 1.3 89.4 - - - +
99F TYR* 1.3 67.3 + - - +
100F ASN 3.3 1.2 + - - -
101F LEU* 4.2 18.4 - - + -
102F THR* 2.7 30.2 + - - +
105F MET* 4.6 15.5 - - + -
106F MET* 4.8 2.5 - - + -
126F THR* 4.2 0.9 - - - -
127F GLU 3.3 7.4 - - - +
142F PHE* 3.7 20.4 - - + +
143F ARG* 4.3 6.5 - - - -
144F VAL* 4.0 30.5 - - + +
264F ILE* 5.1 1.3 - - + -
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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