Contacts of the strand formed by residues 269 - 274 (chain B) in PDB entry 3EWS
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 GLN 269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B MET* 3.0 32.4 + - - +
131B PRO* 4.2 15.8 - - + +
132B GLN 3.0 39.1 + - - +
133B ASN* 3.9 4.0 - - - -
151B ALA* 5.0 2.9 - - - +
155B GLN* 3.3 22.4 + - - +
237B LYS 2.8 16.9 + - - +
238B VAL* 3.6 12.2 - - + +
239B PHE* 2.8 31.8 + - - +
267B ASN 3.0 5.7 + - - -
268B CYS* 1.3 70.5 - - - +
270B MET* 1.3 61.5 + - - +
271B LEU* 4.2 20.8 - - + +
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Residues in contact with MET 270 (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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133B ASN* 2.9 34.0 + - - +
134B LEU 3.3 21.7 + - - -
239B PHE* 3.8 18.8 - - + -
261B GLN* 3.2 29.4 - - - +
264B LEU* 3.5 42.0 - - + -
265B PRO 4.1 8.5 - - - +
266B ARG 5.5 1.1 - - - +
268B CYS* 3.4 19.5 - - + +
269B GLN* 1.3 71.6 - - - +
271B LEU* 1.3 62.7 + - - +
288B VAL 4.6 0.4 - - - +
289B VAL* 3.6 19.4 - - + +
290B PRO* 3.9 13.0 - - + -
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Residues in contact with LEU 271 (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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126B MET* 3.3 48.5 - - + -
134B LEU* 3.8 21.1 - - + +
151B ALA* 4.4 4.5 - - + -
238B VAL* 3.9 19.3 - - + -
239B PHE* 2.7 16.4 + - - +
240B VAL* 3.1 21.6 - - + -
241B LEU* 2.8 24.1 + - - +
269B GLN* 4.2 24.9 - - + +
270B MET* 1.3 78.0 - - - +
272B LEU* 1.3 61.1 + - - +
273B PHE* 3.5 15.9 - - + -
289B VAL* 4.6 1.7 - - - +
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Residues in contact with LEU 272 (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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134B LEU 3.4 6.7 + - - +
135B ILE* 3.4 17.4 - - + -
136B ALA 3.2 22.5 + - - -
241B LEU* 3.7 21.3 - - + +
244B ALA* 4.1 21.1 - - + -
271B LEU* 1.3 75.5 - - - +
273B PHE* 1.3 80.5 + - - +
274B SER* 4.7 4.3 - - - -
281B VAL* 5.3 2.2 - - + -
284B PHE* 4.6 2.0 - - + -
285B ALA* 3.9 35.7 - - + -
288B VAL* 3.9 25.1 - - + -
289B VAL* 3.6 15.5 - - + -
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Residues in contact with PHE 273 (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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122B ALA* 5.2 1.6 - - + -
126B MET* 3.6 34.1 - - + -
134B LEU* 4.7 5.6 - - + -
136B ALA* 3.3 32.8 - - + +
144B LYS* 3.8 41.1 - - + -
147B ALA* 4.6 4.3 - - + -
148B PHE* 3.6 25.4 - + + -
240B VAL* 4.4 7.2 - - + -
241B LEU 3.1 9.3 + - - +
242B ASP* 4.6 4.9 - - - +
243B GLU 3.4 10.9 + - - +
244B ALA 3.1 19.1 + - - -
271B LEU* 3.5 27.1 - - + -
272B LEU* 1.3 85.7 - - - +
274B SER* 1.3 65.9 + - - +
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Residues in contact with SER 274 (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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136B ALA 3.2 5.7 + - - +
137B GLN* 3.0 11.2 - - - -
138B SER 2.7 32.2 + - - +
144B LYS* 3.7 9.0 - - - +
243B GLU* 4.6 2.2 - - - +
244B ALA* 4.2 2.0 - - - +
245B ASP* 3.1 37.0 + - - +
272B LEU* 4.7 3.6 - - - +
273B PHE* 1.3 79.1 - - - +
275B ALA* 1.3 56.0 + - - +
276B THR 3.2 15.2 + - - -
277B PHE* 6.4 0.7 - - - -
281B VAL* 4.0 12.3 - - - +
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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