Contacts of the strand formed by residues 235 - 240 (chain E) in PDB entry 4QY2
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 ASN 235 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C PRO* 3.7 19.3 - - + +
160E THR* 3.8 17.9 - - + +
161E TYR 3.3 5.4 - - - +
162E ARG* 3.1 30.1 - - - +
163E ASN 4.6 0.3 + - - +
199E SER* 3.3 24.3 - - - -
230E VAL* 4.6 1.1 - - - -
233E GLY 4.1 6.7 - - - +
234E ASP* 1.3 91.9 + - - +
236E ILE* 1.3 61.1 + - - +
237E THR* 5.1 0.9 - - - +
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Residues in contact with ILE 236 (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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159E ASN 3.8 1.4 - - - +
160E THR* 3.4 1.3 - - - -
161E TYR* 2.9 54.0 + - + +
171E ILE* 4.0 29.2 - - + -
173E TRP* 5.0 0.4 - - + -
197E VAL* 3.7 29.2 - - + -
198E GLY 3.6 4.7 - - - +
199E SER* 3.9 22.7 - - - +
202E TYR* 4.6 3.8 - - + -
228E THR* 4.6 12.3 - - - +
230E VAL* 3.6 24.7 - - + -
235E ASN* 1.3 76.0 - - - +
237E THR* 1.3 62.9 + - - +
238E PHE* 4.3 9.9 - - + -
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Residues in contact with THR 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C ALA* 3.5 34.0 - - + +
213C ARG* 4.5 2.0 + - - -
214C PRO* 4.3 9.4 - - - +
158E THR* 3.5 24.9 - - + -
159E ASN 3.5 2.9 - - - -
160E THR* 2.9 30.2 + - - +
196E SER 3.5 1.7 - - - +
197E VAL* 3.3 5.7 - - - +
198E GLY 2.9 39.9 + - - -
235E ASN* 5.1 0.3 - - - +
236E ILE* 1.3 73.6 - - - +
238E PHE* 1.3 67.0 + - - +
239E SER 4.7 0.4 - - - +
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Residues in contact with PHE 238 (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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115E PHE* 3.8 27.1 - + + -
158E THR* 3.2 6.4 - - - +
159E ASN* 2.7 42.1 + - + +
171E ILE* 3.6 33.4 - - + -
173E TRP* 3.6 39.3 - + + -
195E ILE* 5.4 0.7 - - + -
196E SER 3.4 2.7 - - - -
197E VAL* 3.5 28.3 - - + -
236E ILE* 4.3 14.4 - - + -
237E THR* 1.3 76.3 - - - +
239E SER* 1.3 59.2 + - - +
240E HIS* 3.6 5.6 - - + -
244E LEU* 4.1 30.7 - - + -
247E PRO* 4.0 9.6 - - + -
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Residues in contact with SER 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C VAL 5.6 0.2 - - - -
211C GLY* 4.8 2.4 - - - -
212C ALA* 4.3 27.8 + - - +
156E GLN* 3.4 18.7 + - - -
157E THR 3.5 5.5 + - - -
158E THR* 4.3 8.3 + - - +
194E SER 3.9 1.0 - - - +
195E ILE* 3.5 1.0 - - - +
196E SER* 2.7 54.0 + - - -
237E THR 4.0 0.2 + - - -
238E PHE* 1.3 73.1 - - - +
240E HIS* 1.3 58.7 + - - +
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Residues in contact with HIS 240 (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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117E TYR* 4.6 0.2 - + - -
145E LEU* 3.5 29.5 - - + +
154E PHE* 4.0 10.4 - + - -
155E PRO 3.6 0.9 - - - +
156E GLN* 3.5 8.8 + - - +
157E THR* 2.9 60.7 + - + +
159E ASN* 3.0 23.0 + - - -
194E SER 3.5 7.2 - - - -
195E ILE* 3.8 21.3 - - + -
238E PHE* 3.6 14.1 - - + -
239E SER* 1.3 74.6 - - - +
241E ASN* 1.3 62.4 + - - +
242E GLY* 4.5 2.3 + - - +
244E LEU* 3.7 32.5 - - + +
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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