Contacts of the strand formed by residues 269 - 273 (chain E) in PDB entry 6IWQ
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 VAL 269 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227E VAL* 4.2 12.6 - - + -
231E ILE* 4.2 3.6 - - + -
242E ILE* 3.4 34.3 - - + +
244E LEU* 4.1 18.2 - - + -
262E ILE* 3.1 48.2 - - + +
265E TRP* 3.7 32.3 + - + +
267E GLY* 4.0 10.7 - - - +
268E LEU* 1.3 81.0 - - + +
270E LYS* 1.3 63.9 + - - +
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Residues in contact with LYS 270 (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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241E GLU* 2.9 44.2 + - - +
242E ILE 3.1 10.4 + - - +
243E VAL* 3.7 11.5 - - + +
244E LEU* 2.9 28.3 + - - +
262E ILE* 4.7 4.3 - - - -
267E GLY 3.3 20.5 + - - +
268E LEU* 4.0 4.0 - - - +
269E VAL* 1.3 76.3 - - - +
271E VAL* 1.3 60.5 + - - +
272E PHE* 4.4 22.7 - - + -
290E LYS 5.8 0.2 - - - +
293E LEU* 4.2 13.1 - - - +
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Residues in contact with VAL 271 (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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215E PHE* 4.5 5.6 - - + -
244E LEU* 3.4 24.5 - - + +
246E ASP* 4.3 8.1 - - + -
258E LEU* 4.5 9.6 - - + -
259E ASP* 3.6 26.0 - - - +
262E ILE* 5.5 6.0 - - + +
270E LYS* 1.3 76.8 - - - +
272E PHE* 1.3 74.7 + - - +
273E ARG* 3.6 37.4 + - - +
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Residues in contact with PHE 272 (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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243E VAL* 3.7 31.6 - - + -
244E LEU 2.9 8.1 + - - -
245E ILE* 3.7 15.5 - - + +
246E ASP 2.9 23.4 + - - +
270E LYS* 4.4 23.3 - - + -
271E VAL* 1.3 80.2 - - - +
273E ARG* 1.3 66.0 + - - +
274E ASN* 4.6 1.5 - - - +
290E LYS* 3.5 64.4 - - + -
292E LYS* 5.7 3.4 - - - -
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Residues in contact with ARG 273 (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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246E ASP* 3.2 26.3 + - - +
254E LEU 2.5 32.5 + - - -
255E LYS* 3.7 12.0 - - - +
256E GLU 4.7 0.2 - - - +
258E LEU* 3.8 18.4 - - - +
259E ASP* 2.8 33.1 + - - -
271E VAL* 3.6 21.4 - - - +
272E PHE* 1.3 80.4 - - - +
274E ASN* 1.3 69.2 + - - +
275E GLU 4.2 0.7 + - - -
290E LYS* 5.4 4.5 - - - -
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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