Contacts of the helix formed by residues 324 - 331 (chain D) in PDB entry 4B6D
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 HIS 324 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300D CYS* 3.2 19.7 - - + +
303D CYS* 3.5 8.7 - - - -
305D LYS* 3.8 14.4 - - + -
306D ARG 3.4 18.8 + - - -
307D ILE* 3.5 23.5 - - + +
312D LEU 4.9 1.1 - - - -
314D LEU* 4.2 0.7 - - - +
323D SER* 1.3 80.3 + - - +
325D PRO* 1.3 71.9 - - + +
326D GLU* 3.5 28.5 - - - +
327D CYS* 3.0 14.5 + - - -
328D ARG* 3.3 9.2 + - - -
1339D ZN 2.1 36.5 - - - -
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Residues in contact with PRO 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D LEU* 3.3 42.2 - - + +
313D SER* 4.6 0.2 - - - -
314D LEU* 3.7 24.9 - - + +
323D SER 3.8 1.8 - - - +
324D HIS* 1.3 85.6 - - + +
326D GLU* 1.3 70.7 + - - +
327D CYS 3.2 0.9 + - - -
328D ARG* 3.5 22.7 + - - +
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Residues in contact with GLU 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D HIS* 3.5 28.7 - - + +
325D PRO* 1.3 88.3 - - - +
327D CYS* 1.3 66.7 + - - +
328D ARG 3.4 0.7 - - - -
329D ASP* 5.2 0.9 + - - +
330D ARG* 5.8 2.3 + - - +
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Residues in contact with CYS 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D CYS* 3.6 11.9 - - - -
302D PRO* 3.3 22.2 - - + +
303D CYS* 4.0 10.1 - - - -
323D SER* 4.4 0.4 - - - -
324D HIS* 3.0 15.5 + - - +
326D GLU* 1.3 86.3 - - - +
328D ARG* 1.3 64.5 + - - +
329D ASP 3.3 3.1 - - - -
330D ARG* 3.1 21.4 + - + +
331D CYS* 3.8 0.2 - - - -
1339D ZN 2.4 35.7 - - - -
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Residues in contact with ARG 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D PHE* 3.5 33.4 - - + -
314D LEU* 3.6 24.2 - - + +
323D SER* 4.0 10.8 - - - -
324D HIS 3.3 2.4 + - - -
325D PRO 3.5 18.2 + - - +
326D GLU 3.4 1.8 - - - -
327D CYS* 1.3 78.4 - - - +
329D ASP* 1.3 79.5 + - - +
330D ARG 3.3 0.7 + - - -
331D CYS* 3.4 18.8 + - - +
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Residues in contact with ASP 329 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326D GLU 5.2 1.0 + - - +
327D CYS 3.3 1.4 + - - -
328D ARG* 1.3 98.9 + - - +
330D ARG* 1.3 62.0 - - + +
331D CYS 3.3 2.8 + - - +
333D LEU* 6.0 1.2 - - - +
326E GLU* 3.8 19.4 - - - +
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Residues in contact with ARG 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D PRO* 3.6 21.8 - - + +
326D GLU 5.8 1.7 + - - +
327D CYS* 3.1 18.0 + - - +
329D ASP* 1.3 81.5 - - + +
331D CYS* 1.3 63.7 + - - +
332D PRO* 3.4 7.4 - - - +
311E LYS* 5.3 5.7 - - - +
312E LEU* 3.4 46.6 - - - +
325E PRO* 4.3 28.4 - - + +
326E GLU* 4.0 16.0 - - - +
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Residues in contact with CYS 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287D HIS* 4.1 20.6 - - + +
289D PHE* 3.7 13.5 - - + -
302D PRO* 3.9 5.4 - - - -
321D VAL* 3.9 10.5 - - + -
323D SER* 3.3 36.1 - - - -
327D CYS 3.8 3.8 - - - -
328D ARG 3.4 18.1 - - - +
329D ASP 3.3 3.1 - - - +
330D ARG* 1.3 76.7 - - - +
332D PRO* 1.3 72.4 - - + +
333D LEU* 3.4 9.2 + - - +
326E GLU* 3.2 13.8 - - - +
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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