Contacts of the helix formed by residues 328 - 339 (chain A) in PDB entry 5HOO
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 LYS 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A TYR* 3.9 26.6 + - - +
286A HIS* 3.9 24.5 - - - +
324A ARG* 2.9 20.7 + - + +
325A GLY* 3.7 7.2 - - - +
326A ILE 3.1 0.8 + - - -
327A HIS* 1.3 75.1 - - - +
329A LEU* 1.3 65.1 + - - +
330A PRO* 3.6 0.9 - - - -
331A GLU* 3.3 41.5 - - - +
332A ARG* 3.4 19.0 + - - +
4E G 4.9 15.0 + - - -
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Residues in contact with LEU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LEU* 4.6 3.6 - - + -
152A ILE* 4.1 26.9 - - + -
247A LEU* 4.8 8.5 - - + -
271A LEU* 6.1 0.2 - - + -
280A LEU* 4.1 22.0 - - + +
282A PRO* 4.1 17.5 - - + -
285A TYR* 3.7 17.3 + - + +
326A ILE* 3.1 25.7 + - + +
328A LYS* 1.3 75.5 - - - +
330A PRO* 1.3 66.5 - - + +
332A ARG* 2.8 24.2 + - - +
333A TRP* 2.9 53.6 + - + +
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Residues in contact with PRO 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU* 3.6 12.7 - - + +
143A TYR* 3.8 39.5 - - + +
149A LEU* 3.7 20.2 - - + -
327A HIS 3.2 18.4 - - - +
329A LEU* 1.3 88.8 - - + +
331A GLU* 1.3 64.3 + - - +
333A TRP* 3.5 22.7 - - + -
334A GLU* 3.2 24.1 + - - +
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Residues in contact with GLU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A HIS 5.0 0.9 + - - +
328A LYS* 3.3 37.8 + - + +
330A PRO* 1.3 79.7 - - - +
332A ARG* 1.3 64.8 + - - +
334A GLU* 3.6 10.5 + - - +
335A LYS* 3.4 46.5 + - - +
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Residues in contact with ARG 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ASP* 2.6 28.8 + - - +
280A LEU* 4.0 9.6 - - + -
285A TYR* 3.5 58.3 - - - +
328A LYS* 3.4 26.0 - - - +
329A LEU* 2.8 9.0 + - + +
331A GLU* 1.3 84.2 - - - +
333A TRP* 1.3 65.5 + - - +
334A GLU 3.2 0.2 - - - -
335A LYS* 3.2 13.1 + - + +
336A CYS* 2.9 24.4 + - - +
344A PHE* 3.1 40.2 - - + -
345A GLU* 2.9 22.7 + - - -
55F G 4.5 5.5 - - - +
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Residues in contact with TRP 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A CYS* 3.6 25.1 - - + +
139A LEU* 3.6 59.2 - - + +
140A LEU* 3.7 19.5 - - + -
143A TYR* 4.1 13.0 - - + -
148A PHE* 4.0 20.9 - + - -
149A LEU* 4.4 6.3 - - + -
152A ILE* 5.4 1.8 - - + -
247A LEU* 6.2 0.7 - - + -
271A LEU* 5.6 3.6 - - + -
280A LEU* 4.3 20.0 - - + +
329A LEU* 2.9 53.0 + - + +
330A PRO* 3.5 26.2 - - + +
331A GLU 3.4 0.2 - - - -
332A ARG* 1.3 77.6 - - - +
334A GLU* 1.3 62.2 + - - +
336A CYS* 3.4 3.9 + - - +
337A VAL* 3.0 27.0 + - - +
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Residues in contact with GLU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU* 3.8 29.3 - - + +
144A LYS* 4.3 10.1 + - - +
330A PRO* 3.2 12.9 + - - +
331A GLU* 3.7 12.3 - - - +
332A ARG 3.2 0.2 - - - -
333A TRP* 1.3 76.0 - - - +
335A LYS* 1.3 60.4 + - + +
337A VAL* 3.2 4.1 + - - +
338A ALA* 2.8 29.6 + - - +
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Residues in contact with LYS 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A GLU* 3.4 40.6 + - - +
332A ARG* 3.2 11.3 + - + +
334A GLU* 1.3 75.5 - - + +
336A CYS* 1.3 53.0 + - - +
338A ALA* 2.9 10.7 + - - +
339A SER* 2.6 40.3 + - - -
344A PHE* 3.6 39.0 - - + -
345A GLU* 5.1 8.7 - - + +
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Residues in contact with CYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ARG* 4.0 27.1 - - - -
133A LYS* 4.4 0.4 - - - -
136A CYS* 2.9 37.7 - - - -
280A LEU* 4.3 2.2 - - + -
332A ARG 2.9 12.4 + - - +
333A TRP* 3.4 5.2 - - - +
335A LYS* 1.3 75.8 - - - +
337A VAL* 1.3 58.2 - - - +
339A SER* 3.3 8.7 + - - -
341A GLY* 3.0 43.2 + - - -
342A LYS 4.6 0.7 - - - -
344A PHE* 3.6 18.9 - - + -
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Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LYS* 3.6 27.6 - - - +
136A CYS* 3.8 4.0 - - + -
137A GLU* 3.7 51.4 - - + +
140A LEU* 3.8 13.2 - - + -
333A TRP 3.0 16.3 + - - +
334A GLU* 3.6 8.1 - - - +
335A LYS 3.2 0.2 - - - -
336A CYS* 1.3 71.4 - - - +
338A ALA* 1.3 65.1 + - - +
340A ASP* 3.2 11.8 + - - +
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Residues in contact with ALA 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A GLU 2.8 14.9 + - - +
335A LYS* 3.4 11.2 - - - +
337A VAL* 1.3 78.8 - - - +
339A SER* 1.3 56.6 + - - +
340A ASP* 3.3 7.4 + - - +
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Residues in contact with SER 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A LYS 2.6 16.0 + - - -
336A CYS 3.7 3.1 - - - -
337A VAL 3.2 0.8 - - - -
338A ALA* 1.3 77.5 - - - +
340A ASP* 1.3 69.5 + - - +
342A LYS* 3.0 47.1 + - - +
344A PHE* 3.4 21.6 - - - +
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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