Contacts of the strand formed by residues 91 - 98 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212D ARG* 4.6 2.9 - - - -
90E SER* 1.3 83.3 + - - +
92E LYS* 1.3 55.8 + - - -
119E GLU 3.6 5.9 + - - -
120E ILE* 3.3 4.2 - - - +
121E ASN* 2.6 40.9 + - - +
277E LYS* 4.4 3.1 - - - -
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Residues in contact with LYS 92 (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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212D ARG* 4.0 37.9 - - - +
216D GLN* 5.6 3.3 - - - +
91E GLY* 1.3 71.0 - - - -
93E ILE* 1.3 72.3 + - - +
94E LYS* 4.0 18.8 - - + +
121E ASN* 3.2 10.1 - - + +
123E GLU* 3.0 34.7 + - + +
139E ASP* 4.2 4.0 - - - +
277E LYS* 2.5 36.7 + - - +
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Residues in contact with ILE 93 (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 LYS* 1.3 81.1 - - - +
94E LYS* 1.3 63.6 + - - +
95E ILE* 3.8 20.0 + - + -
113E PHE* 4.6 2.7 - - + -
120E ILE* 4.0 20.6 - - + -
121E ASN 2.8 8.9 + - - +
122E ILE* 3.5 17.5 - - + +
123E GLU 2.9 26.0 + - - +
139E ASP* 3.6 16.4 - - + -
140E VAL* 5.3 0.7 - - + -
277E LYS* 3.3 47.8 - - + +
278E VAL* 3.9 7.6 - - + +
281E PHE* 4.0 21.1 - - + -
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Residues in contact with LYS 94 (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 LYS* 4.0 24.7 - - + +
93E ILE* 1.3 73.6 - - - +
95E ILE* 1.3 61.5 + - - +
123E GLU* 3.5 25.8 - - + +
137E GLU* 3.7 26.5 + - - +
138E TRP* 3.8 10.4 - - + -
139E ASP* 2.8 59.1 + - - +
140E VAL 3.4 1.6 + - - -
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Residues in contact with ILE 95 (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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93E ILE* 3.8 24.2 - - + +
94E LYS* 1.3 81.0 - - - +
96E SER* 1.3 60.3 + - - +
97E THR* 4.1 11.2 - - + -
110E LEU* 3.7 39.9 - - + -
122E ILE* 4.2 13.7 - - + -
123E GLU 3.0 12.9 + - - +
124E LEU* 4.3 7.2 - - + -
125E THR 3.1 22.3 + - - -
138E TRP* 3.6 9.0 - - - -
140E VAL* 3.1 14.8 - - + +
142E PHE* 4.1 16.4 - - + -
281E PHE* 4.1 15.9 - - + -
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Residues in contact with SER 96 (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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95E ILE* 1.3 73.4 - - - +
97E THR* 1.3 64.8 + - - +
125E THR 3.3 11.1 + - - -
127E GLU* 4.0 8.8 - - - +
133E LEU* 3.7 21.5 - - - +
138E TRP* 3.8 28.1 - - - -
140E VAL 3.1 5.9 + - - -
141E ILE* 4.2 13.9 - - - +
142E PHE* 2.8 34.4 + - - +
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Residues in contact with THR 97 (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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95E ILE* 4.1 9.6 - - + -
96E SER* 1.3 80.6 + - - +
98E PRO* 1.3 70.3 - - - +
102E THR* 2.7 33.6 + - + +
106E MET* 4.5 10.8 - - + -
110E LEU* 4.8 0.9 - - + -
124E LEU* 3.8 24.9 - - + +
125E THR 3.0 4.2 + - - -
126E THR* 3.2 10.0 - - - +
127E GLU* 2.9 27.1 + - - +
142E PHE* 3.6 20.2 - - + -
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Residues in contact with PRO 98 (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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97E THR* 1.3 87.4 - - - +
99E TYR* 1.3 69.5 + - - +
101E LEU* 3.3 19.6 + - + -
102E THR* 2.6 31.0 + - - +
105E MET* 4.7 8.7 - - + -
106E MET* 4.8 8.7 - - + -
126E THR* 4.7 0.2 - - - -
127E GLU 3.5 8.5 - - - +
142E PHE* 3.3 27.8 - - + +
143E ARG* 4.2 8.7 - - - -
144E VAL* 4.3 16.4 - - + +
264E ILE* 4.9 1.8 - - + -
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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