Contacts of the strand formed by residues 410 - 414 (chain B) in PDB entry 4IYM
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 GLY 410 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B LYS 5.0 0.2 - - - +
250B ASN* 3.0 42.9 + - - +
251B HIS 4.1 0.7 + - - -
280B MSE 3.9 11.0 - - - -
408B GLY* 5.5 0.2 - - - -
409B ASN* 1.3 80.8 + - - +
411B VAL* 1.3 62.9 + - - +
430B ILE* 3.6 10.2 - - - +
432B MSE 3.2 10.3 - - - -
440B PRO* 4.8 0.7 - - - -
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Residues in contact with VAL 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ASN* 5.1 0.7 - - - -
251B HIS* 3.4 17.0 - - + +
253B ILE* 4.6 0.2 - - + -
282B ILE* 5.3 1.7 - - - +
402B PRO* 3.9 22.7 - - + -
410B GLY* 1.3 75.0 - - - +
412B ALA* 1.3 66.0 + - - +
424B PHE* 3.8 25.4 - - + -
428B ILE* 4.0 10.1 - - + -
430B ILE* 3.7 25.8 - - + -
432B MSE 3.1 2.5 + - - +
433B VAL* 3.5 26.7 - - + -
434B GLY 2.8 23.6 + - - -
440B PRO* 3.7 6.5 - - - +
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Residues in contact with ALA 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B HIS 2.9 9.3 + - - +
252B MSE 3.3 19.4 - - + -
253B ILE* 2.8 34.0 + - - +
282B ILE* 4.7 1.6 - - + -
411B VAL* 1.3 78.9 - - - +
413B ILE* 1.3 54.8 + - - +
414B TYR* 4.3 5.2 - - + -
424B PHE* 4.4 1.7 - - - -
434B GLY 3.2 5.4 - - - +
437B VAL 3.3 26.2 - - - +
438B PRO* 4.3 11.7 - - + +
440B PRO* 5.3 0.2 - - + -
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Residues in contact with ILE 413 (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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253B ILE* 3.3 18.2 - - + +
255B MSE 4.1 16.8 - - + -
395B TYR* 4.4 6.3 - - + -
412B ALA* 1.3 73.9 - - - +
414B TYR* 1.3 74.1 + - - +
415B THR* 4.1 5.8 + - + +
420B ALA 4.0 15.0 - - - +
421B ALA* 4.4 13.7 - - + +
424B PHE* 3.7 52.7 - - + -
433B VAL* 5.4 0.9 - - + -
434B GLY 2.8 17.1 + - - +
435B VAL* 3.6 12.2 - - + +
436B ASN* 2.9 23.4 + - - +
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Residues in contact with TYR 414 (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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252B MSE 3.7 29.8 - - + -
253B ILE 2.8 13.4 + - - +
254B ILE* 4.4 8.7 - - + -
255B MSE 2.8 31.2 + - - +
258B ALA* 3.3 15.5 - - + +
259B ASP* 4.6 6.3 - - + -
262B GLN* 4.2 11.0 - - + -
263B ALA* 3.8 33.2 - - + -
266B ALA* 3.4 14.5 - - + +
412B ALA* 4.3 1.3 - - + -
413B ILE* 1.3 78.2 - - - +
415B THR* 1.3 62.6 + - - +
436B ASN* 3.1 37.7 + - + +
437B VAL 3.6 12.1 - - - -
438B PRO* 3.2 27.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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