Contacts of the strand formed by residues 350 - 357 (chain B) in PDB entry 3Q41
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 350 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B LEU* 3.9 5.0 - - - +
272B ILE* 3.0 49.6 + - + +
335B THR 5.2 8.3 + - - -
336B GLY* 5.8 1.4 + - - -
348B PHE 4.3 4.6 - - - +
349B ALA* 1.3 78.2 - - - +
351B TYR* 1.3 62.0 + - - +
366B ILE* 5.0 6.6 - - + +
367B TYR 3.3 7.0 - - - +
368B ASN* 3.2 29.4 + - + +
369B GLY 4.3 1.0 + - - -
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Residues in contact with TYR 351 (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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124B ARG* 4.0 15.9 - - - -
142B PRO* 3.5 22.0 - - + +
143B PRO 4.8 0.3 + - - -
146B HIS* 3.8 19.1 + - - +
147B GLN* 4.0 16.4 - - + -
150B VAL* 3.6 25.1 - - + -
269B LEU* 3.6 29.6 - - + -
270B GLN 3.3 7.4 - - - +
271B LEU* 3.7 31.6 - - + -
272B ILE* 3.7 2.0 - - - -
349B ALA* 3.8 16.9 - - + +
350B ASN* 1.3 73.9 - - - +
352B SER* 1.3 60.7 + - - +
353B ILE 3.6 0.5 + - - -
366B ILE* 3.7 1.6 - - - +
367B TYR* 2.9 52.4 + + + +
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Residues in contact with SER 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B LEU* 4.6 0.9 - - - -
270B GLN* 2.8 40.9 + - - +
272B ILE* 3.4 23.9 - - - +
351B TYR* 1.3 71.8 - - - +
353B ILE* 1.3 63.4 + - - +
354B MET* 3.4 19.4 + - - +
363B GLN* 4.0 25.9 + - - -
365B GLY 4.0 3.4 - - - -
366B ILE* 4.5 1.8 - - - +
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Residues in contact with ILE 353 (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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150B VAL* 4.7 4.3 - - + -
154B MET* 3.8 33.9 - - + -
158B TYR* 6.0 1.3 - - - +
267B ILE* 3.9 10.5 - - + -
268B GLY 3.9 6.3 - - - +
269B LEU* 4.7 10.1 - - + +
351B TYR 4.2 0.9 - - - +
352B SER* 1.3 68.5 - - - +
354B MET* 1.3 61.6 + - - +
363B GLN* 3.4 8.0 - - - -
364B VAL* 3.2 44.3 + - + -
365B GLY* 3.1 17.7 + - - +
366B ILE 3.5 10.5 - - - +
367B TYR* 3.4 35.4 - - + +
372B VAL* 3.8 18.2 - - + -
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Residues in contact with MET 354 (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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254B ILE* 4.0 11.4 - - + -
267B ILE* 3.4 14.6 - - - +
268B GLY 2.9 27.9 + - - +
269B LEU 4.4 1.1 - - - -
270B GLN* 4.0 34.5 - - + +
352B SER* 3.4 29.8 - - - +
353B ILE* 1.3 81.4 - - - +
355B ASN* 1.3 62.7 + - - +
361B LEU* 3.3 52.0 - - + +
362B VAL 3.8 2.0 - - - +
363B GLN* 4.0 15.9 - - + +
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Residues in contact with ASN 355 (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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265B GLY* 3.6 7.1 - - - -
266B ILE 3.4 12.3 - - - +
267B ILE* 3.5 16.8 - - + +
354B MET* 1.3 78.8 - - - +
356B LEU* 1.3 65.7 + - - +
357B GLN* 3.3 36.0 + - - +
360B LYS 3.2 4.3 - - - +
361B LEU* 4.3 4.2 - - - +
362B VAL* 3.0 29.6 + - - +
364B VAL* 3.8 20.5 - - + +
379B ILE* 3.5 9.5 - - - +
380B ILE 3.3 27.1 + - - +
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Residues in contact with LEU 356 (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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254B ILE* 6.4 0.2 - - + -
259B LEU* 3.6 26.7 - - + -
262B ALA* 3.8 18.8 - - + -
263B PRO 3.6 11.9 - - - +
264B ASP* 3.1 10.6 - - - +
265B GLY* 2.8 30.4 + - - +
266B ILE* 3.3 20.7 + - + -
355B ASN* 1.3 73.6 + - - +
357B GLN* 1.3 59.8 + - - +
359B ARG* 3.4 41.3 - - - +
360B LYS 3.7 26.9 - - - +
361B LEU* 4.0 11.7 - - + +
380B ILE* 4.1 2.8 - - - +
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Residues in contact with GLN 357 (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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264B ASP* 4.0 0.2 - - - -
355B ASN* 3.3 11.4 - - - +
356B LEU* 1.3 70.7 - - - +
358B ASN* 1.3 67.6 + - - +
359B ARG 3.2 0.9 - - - -
360B LYS* 2.8 39.2 + - - +
362B VAL* 3.3 28.0 - - + +
377B ARG* 3.6 24.2 + - - +
378B LYS 3.0 23.6 + - - -
379B ILE 3.9 0.4 - - - -
380B ILE* 3.2 45.6 - - + +
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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