Contacts of the strand formed by residues 153 - 160 (chain B) 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 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B LEU* 1.3 72.2 - - - +
154B ALA* 1.3 65.0 + - - +
155B ARG* 5.6 2.5 - - + -
266B MET 3.5 2.1 - - - +
267B LEU* 3.2 24.1 - - - -
268B TYR* 2.8 61.8 + - + +
269B ASN 4.7 2.5 - - - +
270B HIS* 3.3 38.8 - - + +
134E ASP* 3.2 33.4 - - + +
136E THR* 3.7 6.3 - - - +
137E GLU* 4.0 17.3 - - + +
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Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU 3.5 6.5 + - - +
153B ILE* 1.3 78.8 - - - +
155B ARG* 1.3 62.4 + - - +
156B LYS 4.3 0.2 - - - -
265B TYR* 4.3 13.9 - - + -
266B MET 3.6 4.3 - - - -
267B LEU* 3.6 19.5 - - + -
132E GLN* 4.5 8.5 - - - +
133E LEU 6.1 0.2 - - - -
134E ASP* 4.9 7.3 + - - +
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Residues in contact with ARG 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ILE* 5.6 2.2 - - + -
154B ALA* 1.3 76.4 - - - +
156B LYS* 1.3 75.6 + - - +
157B ILE* 3.5 10.1 + - + +
265B TYR* 3.8 3.5 - - - -
266B MET* 2.9 43.0 + - + +
268B TYR* 5.5 5.8 - - + -
286B ILE* 3.7 48.1 + - + +
127E GLU* 2.7 39.4 + - - -
129E ASN* 4.8 4.6 + - - +
132E GLN* 3.7 40.8 + - - +
133E LEU* 4.5 4.8 - - - +
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Residues in contact with LYS 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ARG* 1.3 83.1 + - - +
157B ILE* 1.3 64.3 + - - +
158B GLY* 3.7 18.6 + - - +
159B SER* 4.6 5.5 + - - -
263B ASP* 2.7 39.6 + - + +
264B ILE 3.4 12.3 - - - +
265B TYR* 3.6 15.8 - - + +
132E GLN* 2.9 38.9 + - + +
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Residues in contact with ILE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B MET* 6.2 2.5 - - + -
106B MET* 4.6 9.4 - - - -
109B MET* 5.0 5.4 - - + -
142B PHE* 3.8 31.9 - - + -
155B ARG* 3.7 12.8 - - + +
156B LYS* 1.3 80.2 - - - +
158B GLY* 1.3 55.0 + - - +
264B ILE* 2.7 38.7 + - + +
265B TYR 4.4 1.3 - - - +
266B MET* 4.2 13.0 - - + +
285B VAL* 4.0 27.1 - - + +
286B ILE* 5.7 2.9 - - - -
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Residues in contact with GLY 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B MET* 6.0 2.2 - - - -
156B LYS* 3.7 15.5 - - - +
157B ILE* 1.3 79.2 - - - +
159B SER* 1.3 61.0 + - - -
263B ASP* 3.5 2.6 - - - -
264B ILE* 2.7 36.7 + - - +
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Residues in contact with SER 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B MET* 4.8 6.4 - - - +
156B LYS* 4.6 4.9 + - - -
158B GLY* 1.3 76.7 - - - -
160B VAL* 1.3 66.1 + - - +
238B ASP* 5.3 0.3 - - - +
239B VAL* 5.7 2.1 - - - +
261B PRO* 5.6 6.1 - - - -
262B ARG 3.4 13.9 - - - -
263B ASP* 3.7 15.0 - - - +
264B ILE* 4.3 6.1 - - - +
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Residues in contact with VAL 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LEU* 4.4 9.4 - - + -
105B MET* 4.9 1.1 - - + -
144B VAL* 4.1 14.1 - - + -
159B SER* 1.3 79.0 - - - +
161B LYS* 1.3 62.6 + - - +
162B ASP* 4.3 5.6 + - - +
237B PRO* 3.6 33.4 - - + -
238B ASP* 4.0 11.4 - - - +
239B VAL* 4.3 12.1 - - + -
261B PRO* 3.4 2.4 - - - +
262B ARG* 3.0 37.5 + - + +
264B ILE* 3.9 22.9 - - + -
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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