Contacts of the helix formed by residues 349 - 355 (chain B) in PDB entry 4U1D
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 LEU 349 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346B ASP* 3.2 23.5 + - + +
347B PRO 3.2 3.0 + - - -
348B HIS* 1.3 74.8 - - - +
350B ARG* 1.3 69.5 + - + +
351B MET 3.0 3.1 + - - -
352B TYR* 3.3 21.2 + - + +
353B ARG* 4.2 20.1 + - - +
360B LYS* 3.8 35.2 - - + +
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Residues in contact with ARG 350 (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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211A ASP* 5.1 13.5 + - - +
257B TYR* 5.6 1.8 - - - +
261B GLU* 6.1 1.3 - - - -
345B TYR* 5.8 1.4 + - - -
347B PRO* 3.8 21.4 + - - +
348B HIS 3.3 0.9 - - - -
349B LEU* 1.3 79.9 - - + +
351B MET* 1.3 57.4 + - - +
353B ARG* 3.1 31.1 + - - +
354B LEU* 3.0 41.3 + - + +
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Residues in contact with MET 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B TYR* 3.4 44.8 + - + +
260B ILE* 4.0 28.7 - - + -
261B GLU* 4.7 2.9 - - - +
290B PHE* 3.6 23.6 - - + -
298B LEU* 3.7 11.7 - - + -
348B HIS 3.3 14.7 + - - +
349B LEU 3.0 0.8 - - - -
350B ARG* 1.3 80.6 - - + +
352B TYR* 1.3 61.0 + - - +
354B LEU* 3.0 29.6 + - + +
355B LEU* 3.0 49.8 + - + +
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Residues in contact with TYR 352 (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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295B ASP* 4.6 10.1 + - - +
296B PRO* 5.4 1.2 - - - +
297B LEU* 3.8 28.5 + - + +
298B LEU* 3.5 36.8 + - + +
346B ASP* 3.7 14.8 + - - -
348B HIS* 3.7 11.7 - - + -
349B LEU* 3.3 17.6 + - + +
350B ARG 3.2 0.4 - - - -
351B MET* 1.3 77.3 - - - +
353B ARG* 1.3 63.7 + - + +
355B LEU* 3.2 8.5 + - - +
357B LEU* 3.2 36.0 + - + +
359B ALA 4.8 1.1 - - - -
360B LYS* 3.6 57.8 + - + +
361B PRO* 3.8 18.6 - - + -
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Residues in contact with ARG 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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265A HIS* 4.1 28.0 - - - -
350A ARG* 4.2 21.7 + - - +
264B PHE* 4.4 5.3 - - - -
349B LEU* 4.7 19.6 + - - +
350B ARG* 3.1 38.3 + - - +
352B TYR* 1.3 77.8 - - + +
354B LEU* 1.3 66.7 + - + +
355B LEU 3.3 0.9 + - - -
356B ASN* 3.3 13.2 + - - +
357B LEU 3.9 9.9 - - - +
358B ASP 5.2 4.3 - - - +
359B ALA* 5.8 3.4 - - - -
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Residues in contact with LEU 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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261B GLU* 3.8 25.4 - - + -
264B PHE* 3.1 63.9 - - + +
265B HIS* 5.4 3.1 - - + -
350B ARG* 3.0 32.1 + - + +
351B MET* 3.0 46.6 + - + +
353B ARG* 1.3 81.8 - - + +
355B LEU* 1.3 57.8 + - + +
356B ASN* 3.3 4.4 + - - +
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Residues in contact with LEU 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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260B ILE* 5.7 0.4 - - + -
283B TYR* 5.9 1.3 - - + -
286B LEU* 4.8 14.8 - - + -
290B PHE* 4.6 10.5 - - + -
298B LEU* 4.0 20.4 - - + +
301B THR* 3.5 29.6 - - + -
302B ALA* 4.7 3.8 - - - +
305B LYS* 3.5 25.3 - - + +
351B MET* 3.0 52.3 + - + +
352B TYR* 3.2 5.6 + - - +
353B ARG 3.2 1.4 - - - -
354B LEU* 1.3 77.8 - - - +
356B ASN* 1.3 66.0 + - - +
357B LEU* 3.0 21.2 + - + +
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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