Contacts of the strand formed by residues 122 - 127 (chain A) 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 ILE 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A LYS* 5.0 0.4 - - - -
93A ILE* 3.5 27.4 - - + +
95A ILE* 3.7 29.8 - - + -
110A LEU* 4.9 4.5 - - + -
113A PHE* 4.1 24.7 - - + -
114A MET* 4.1 23.8 - - + -
120A ILE 4.9 1.6 - - - +
121A ASN* 1.3 76.8 - - - +
123A GLU* 1.3 67.9 - - - +
124A LEU 4.3 0.2 - - - +
281A PHE* 4.6 5.2 - - + -
213B GLY 4.7 1.6 - - - +
214B ARG 2.9 7.2 + - - +
215B PHE* 3.3 28.7 - - + -
216B GLN 2.8 29.6 + - - -
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Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LYS* 3.3 41.7 - - + +
93A ILE 2.9 9.1 + - - +
94A LYS* 3.5 20.8 + - + +
95A ILE* 3.0 28.2 + - - +
122A ILE* 1.3 74.8 - - - +
124A LEU* 1.3 58.2 + - - +
125A THR* 5.2 1.8 - - - +
212B ARG* 4.9 10.0 + - + +
216B GLN* 3.3 40.2 + - + +
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ILE* 3.6 18.6 - - + +
97A THR* 3.3 38.4 - - + +
102A THR* 4.1 22.2 - - + -
107A MET* 4.3 2.5 - - - -
110A LEU* 4.1 13.9 - - + -
122A ILE* 4.5 0.4 - - + -
123A GLU* 1.3 74.3 - - - +
125A THR* 1.3 73.4 + - - +
126A THR* 4.7 3.1 - - + +
215B PHE* 3.7 32.5 - - + -
216B GLN 2.6 15.2 + - - +
217B ALA* 3.1 24.9 - - + -
218B ASN* 3.2 6.8 + - - +
222B VAL* 4.5 6.3 - - + -
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Residues in contact with THR 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LYS* 5.3 3.6 + - - +
95A ILE 3.1 6.7 + - - -
96A SER* 3.4 7.0 + - - -
97A THR 3.2 19.4 + - - -
123A GLU* 5.2 1.2 - - - +
124A LEU* 1.3 81.1 + - - +
126A THR* 1.3 69.4 + - - +
127A GLU* 3.5 8.0 + - - +
138A TRP* 3.7 31.1 - - + -
218B ASN* 3.2 24.5 - - + +
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Residues in contact with THR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A THR* 3.2 10.8 - - - +
99A TYR* 3.5 37.4 - - + +
102A THR* 4.0 24.9 - - + +
124A LEU* 4.2 5.1 - - + -
125A THR* 1.3 76.4 - - - +
127A GLU* 1.3 59.8 + - - +
99B TYR* 4.5 2.9 + - - -
218B ASN* 2.8 37.4 + - - +
219B ALA* 4.5 14.8 - - + +
222B VAL* 5.4 5.4 - - + -
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Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A SER* 3.2 26.9 - - - +
97A THR 2.7 11.1 + - - +
98A PRO* 3.4 7.6 - - - +
99A TYR* 3.0 21.3 + - - +
125A THR* 4.1 7.9 - - + +
126A THR* 1.3 77.4 - - - +
128A SER* 1.3 74.0 + - - +
129A ASN* 2.9 41.7 + - - +
130A ALA* 4.3 4.4 - - + +
133A LEU* 4.0 25.4 - - + +
138A TRP* 5.7 0.9 - - - -
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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