Contacts of the helix formed by residues 330 - 341 (chain A) in PDB entry 4QBT
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 THR 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A GLU 5.5 0.2 - - - +
327A LYS 3.8 10.3 - - - +
328A PHE 3.1 2.2 + - - +
329A ASN* 1.3 81.5 - - - +
331A PRO* 1.4 73.7 - - + +
332A ALA* 4.3 4.9 - - - +
333A LEU* 3.1 34.3 + - + +
334A LYS* 3.2 30.1 + - - +
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Residues in contact with PRO 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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330A THR* 1.4 88.1 - - + +
332A ALA* 1.3 61.4 + - + +
333A LEU 3.2 0.2 - - - -
334A LYS* 3.4 11.5 + - + +
335A LYS* 2.9 29.5 + - - +
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Residues in contact with ALA 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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330A THR* 3.4 6.2 - - - +
331A PRO* 1.3 81.7 - - + +
333A LEU* 1.3 62.3 + - + +
335A LYS* 3.3 8.3 - - - +
336A LEU* 2.8 28.4 + - - +
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Residues in contact with LEU 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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96A TYR* 5.5 0.5 - - - -
99A ASN* 4.0 17.0 - - + +
327A LYS* 3.4 22.9 - - + +
328A PHE* 3.9 41.3 - - + +
330A THR* 3.1 22.2 + - + +
331A PRO 3.2 0.6 - - - -
332A ALA* 1.3 81.4 - - + +
334A LYS* 1.3 53.2 + - - +
336A LEU* 3.2 27.7 + - + +
337A ALA* 2.7 36.6 + - - +
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Residues in contact with LYS 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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328A PHE 4.5 4.8 + - - +
329A ASN* 3.2 29.5 + - - +
330A THR 3.2 20.9 + - - +
331A PRO* 3.5 11.8 - - + +
332A ALA 3.3 0.2 - - - -
333A LEU* 1.3 73.0 - - - +
335A LYS* 1.3 56.6 + - - +
337A ALA* 3.7 6.2 - - - +
338A SER* 2.8 37.6 + - - -
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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 PRO 2.9 16.0 + - - +
332A ALA* 3.3 14.6 - - - +
334A LYS* 1.3 74.8 - - - +
336A LEU* 1.3 53.5 + - - +
338A SER* 3.6 3.3 - - - -
339A ALA* 2.7 42.2 + - + +
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Residues in contact with LEU 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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92A LEU* 3.3 44.9 - - + +
95A SER* 4.1 11.0 - - - +
96A TYR* 3.9 21.3 - - + +
99A ASN* 3.2 31.0 - - - +
328A PHE* 6.2 0.2 - - + -
332A ALA 2.8 14.7 + - - +
333A LEU* 3.2 20.0 - - + +
335A LYS* 1.3 74.9 - - - +
337A ALA* 1.3 52.8 + - - +
339A ALA* 3.6 4.1 - - - +
340A ALA* 2.6 39.4 + - + +
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Residues in contact with ALA 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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47A LYS* 5.2 6.6 + - - +
96A TYR* 4.2 26.9 - - + +
235A LEU* 5.5 6.5 - - + -
328A PHE* 5.8 0.9 - - + -
333A LEU 2.7 20.1 + - - +
334A LYS* 3.7 7.9 - - - +
336A LEU* 1.3 72.7 - - - +
338A SER* 1.3 58.9 + - - +
340A ALA* 3.3 3.8 + - - +
341A TYR* 2.9 34.2 + - - +
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Residues in contact with SER 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 LYS 2.8 21.8 + - - -
335A LYS* 3.6 3.6 - - - -
337A ALA* 1.3 70.1 - - - +
339A ALA* 1.3 64.7 + - - +
341A TYR 3.0 26.4 + - - +
342A PRO* 3.3 11.1 - - - +
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Residues in contact with ALA 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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89A LEU* 3.7 20.3 - - - +
92A LEU* 4.3 22.0 - - + -
335A LYS* 2.7 27.8 + - + +
336A LEU* 3.6 4.5 - - - +
338A SER* 1.3 75.1 - - - +
340A ALA* 1.3 60.2 + - - +
342A PRO* 4.2 9.6 - - - +
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Residues in contact with ALA 340 (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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89A LEU* 5.0 5.3 - - - +
92A LEU* 4.3 19.9 - - - +
93A ARG* 3.0 41.3 + - + -
96A TYR* 4.4 6.3 - - + -
336A LEU* 2.6 24.1 + - + +
337A ALA* 3.6 3.4 - - - +
339A ALA* 1.3 74.2 - - - +
341A TYR* 1.3 81.5 + - + +
342A PRO* 3.7 3.5 - - - +
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Residues in contact with TYR 341 (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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45A THR 3.0 21.3 + - - -
46A GLY* 4.0 2.7 - - - -
47A LYS* 3.4 55.7 + - + +
93A ARG* 3.3 42.4 - - + +
96A TYR* 3.6 20.0 - + - -
97A TYR* 3.3 22.0 - - - -
337A ALA 2.9 16.2 + - - +
338A SER* 3.0 13.0 + - - +
340A ALA* 1.3 89.2 - - + +
342A PRO* 1.4 63.8 - - - +
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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