Contacts of the strand formed by residues 402 - 409 (chain B) in PDB entry 4RE1
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 402 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B PHE* 3.6 4.0 - - - +
276B TRP* 2.7 43.6 + - + +
395B SER* 4.8 1.7 + - - -
397B SER* 3.7 24.3 + - - -
400B GLY 3.6 10.2 + - - +
401B ALA* 1.3 80.1 - - - +
403B HIS* 1.3 67.9 + - - +
98C PRO* 3.6 19.6 - - - +
99C PRO* 2.9 48.8 + - + +
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Residues in contact with HIS 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B HIS 3.4 25.6 + - - -
227B ILE* 4.1 22.2 - - + +
228B GLY 5.1 1.8 - - - -
273B VAL* 4.2 4.5 - - + -
274B LYS 3.1 13.0 - - - +
275B PHE* 3.9 16.0 - - + -
276B TRP* 4.2 5.4 - - - -
402B GLN* 1.3 82.1 - - - +
404B HIS* 1.3 68.6 + - - +
405B ILE* 3.8 33.4 - - + +
99C PRO* 4.0 8.7 - - - +
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Residues in contact with HIS 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B GLU* 5.6 0.6 + - - -
272B LEU 3.9 0.7 - - - +
273B VAL* 3.4 5.2 - - - +
274B LYS* 2.9 34.5 + - + +
276B TRP* 3.5 21.8 - + - -
403B HIS* 1.3 76.4 + - - +
405B ILE* 1.3 63.1 + - - +
406B TYR* 3.4 28.5 - + + +
94C SER* 3.3 34.1 + - - -
97C LYS 3.2 18.4 + - - -
99C PRO* 3.5 28.8 - - + +
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Residues in contact with ILE 405 (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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195B SER* 3.8 20.6 - - - +
196B ILE* 3.8 42.8 - - + -
227B ILE* 4.8 6.7 - - + -
239B LEU* 3.6 34.3 - - + +
240B GLU 4.2 3.3 + - - +
271B PHE* 4.0 17.3 - - + -
272B LEU 3.6 4.9 - - - +
273B VAL* 4.3 7.4 - - + -
403B HIS* 3.8 27.6 - - + +
404B HIS* 1.3 78.9 + - - +
406B TYR* 1.3 71.2 + - - +
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Residues in contact with TYR 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B LEU* 4.9 0.7 - - - -
240B GLU* 3.2 35.9 - - + +
242B VAL* 3.8 27.1 - - + -
271B PHE* 3.3 11.3 - - - +
272B LEU* 2.7 59.1 + - + +
274B LYS* 4.3 3.1 - - + -
404B HIS* 3.4 33.3 - + + +
405B ILE* 1.3 76.3 - - - +
407B ARG* 1.3 63.0 + - - +
92C PRO* 3.8 11.7 - - + -
94C SER* 2.9 28.2 + - - -
95C PHE* 3.3 40.6 - + - -
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Residues in contact with ARG 407 (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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300A SER* 5.8 1.8 + - - -
195B SER 5.2 2.8 + - - -
197B GLY 4.8 7.3 + - - -
239B LEU* 4.1 33.5 - - + +
240B GLU 3.0 10.3 + - - +
241B SER* 3.2 9.0 - - - -
242B VAL 2.8 27.4 + - - -
268B ASN* 3.6 43.7 + - - +
270B PHE 3.9 5.6 + - - +
271B PHE* 3.9 18.6 - - + -
406B TYR* 1.3 71.7 - - - +
408B LEU* 1.3 63.1 + - - +
409B VAL* 4.6 9.9 - - + -
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Residues in contact with LEU 408 (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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242B VAL* 3.5 23.6 - - + +
244B ILE* 4.2 27.8 - - + -
247B ILE* 3.8 27.8 - - + -
258B LEU* 5.2 3.4 - - + -
262B PHE* 3.7 13.0 - - + -
267B GLN* 3.7 13.3 - - - +
270B PHE* 3.1 26.6 + - + +
271B PHE 3.5 33.7 - - - +
272B LEU* 3.7 18.2 - - + +
387B CYS* 5.9 0.4 - - - -
389B ALA* 4.5 5.2 - - + +
406B TYR 3.7 0.4 + - - -
407B ARG* 1.3 73.6 - - - +
409B VAL* 1.3 61.3 + - - +
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Residues in contact with VAL 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B SER* 3.9 28.0 - - - +
242B VAL 2.9 24.4 + - - +
243B ASP* 3.6 4.7 - - - +
244B ILE* 2.9 27.2 + - - +
262B PHE* 3.9 8.3 - - - -
267B GLN* 5.3 1.8 - - - -
407B ARG* 4.0 9.9 - - + +
408B LEU* 1.3 79.5 - - - +
410B LYS* 1.3 62.5 + - - +
411B ASP* 4.5 11.9 - - - +
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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