Contacts of the helix formed by residues 393 - 403 (chain A) in PDB entry 4LBD
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 GLY 393 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A 961 3.6 17.7 - - - +
268A LEU* 4.0 6.5 - - - -
272A MET* 3.9 10.5 - - - -
307A LEU* 3.7 18.4 - - - +
389A ILE 3.0 10.1 + - - -
390A SER 2.9 8.0 + - - -
392A LYS* 1.3 76.2 - - - +
394A ALA* 1.3 62.2 + - - +
396A ARG* 3.3 0.5 + - - +
397A ALA* 3.0 18.7 + - - +
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Residues in contact with ALA 394 (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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268A LEU* 3.7 6.4 - - + +
390A SER 2.8 11.7 + - - +
391A THR* 3.6 11.7 - - + +
393A GLY* 1.3 74.8 - - - +
395A GLU* 1.3 60.3 + - + +
397A ALA* 2.9 19.8 + - - +
398A ILE* 3.2 16.1 + - - +
416A LEU* 4.2 21.7 - - + +
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Residues in contact with GLU 395 (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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391A THR* 2.9 28.1 + - - +
392A LYS* 3.4 18.0 - - - +
394A ALA* 1.3 78.0 - - + +
396A ARG* 1.3 60.7 + - - +
398A ILE* 3.1 26.9 + - + +
399A THR* 3.5 8.7 + - - -
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Residues in contact with ARG 396 (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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1A 961 4.1 15.7 - - + -
221A GLN 4.6 6.1 + - - -
303A GLY* 2.9 28.2 + - - +
304A PHE 3.8 18.0 + - - +
305A GLY* 3.8 8.9 - - - -
306A PRO* 3.9 28.0 - - - +
307A LEU* 4.3 9.2 - - + -
392A LYS 2.8 16.8 + - - +
393A GLY* 3.6 9.0 - - - +
394A ALA 3.1 0.2 - - - -
395A GLU* 1.3 78.1 - - - +
397A ALA* 1.3 56.4 + - - +
398A ILE 3.2 0.3 + - - -
399A THR* 3.2 36.5 + - - +
400A LEU* 3.0 37.6 + - + +
403A GLU* 2.8 31.0 + - - -
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Residues in contact with ALA 397 (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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1A 961 4.0 15.3 - - + -
393A GLY 3.0 12.6 + - - +
394A ALA 2.9 12.1 + - - +
396A ARG* 1.3 77.2 - - - +
398A ILE* 1.3 60.3 + - - +
400A LEU* 3.8 9.0 - - - +
401A LYS* 3.0 33.1 + - - +
408A MET* 3.8 3.2 - - + +
416A LEU* 3.7 34.5 - - + -
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Residues in contact with ILE 398 (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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394A ALA 3.2 11.8 + - - +
395A GLU* 3.3 20.4 - - + +
396A ARG 3.1 0.6 - - - -
397A ALA* 1.3 79.3 - - - +
399A THR* 1.3 63.4 + - - +
401A LYS* 3.5 23.9 + - + +
402A MET* 3.4 23.2 - - + +
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Residues in contact with THR 399 (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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395A GLU 3.5 11.3 + - - -
396A ARG* 3.2 29.1 + - - +
398A ILE* 1.3 75.9 - - - +
400A LEU* 1.3 65.8 + - - +
402A MET* 2.9 37.5 + - + +
403A GLU* 3.4 15.9 + - + +
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Residues in contact with LEU 400 (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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1A 961 3.7 35.0 - - + -
222A LEU* 4.2 7.9 - - + -
227A TRP* 3.7 21.1 - - + -
303A GLY* 3.7 30.3 - - - +
396A ARG* 3.0 20.3 + - - +
397A ALA 3.8 6.1 - - - +
399A THR* 1.3 79.8 - - - +
401A LYS* 1.3 61.9 + - - +
403A GLU* 3.0 22.8 + - - +
404A ILE* 2.9 46.2 + - + +
408A MET* 3.8 5.8 - - + -
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Residues in contact with LYS 401 (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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397A ALA* 3.0 25.7 + - - +
398A ILE* 3.6 24.9 - - + +
399A THR 3.1 0.8 + - - -
400A LEU* 1.3 77.3 - - - +
402A MET* 1.3 63.3 + - - +
404A ILE* 3.5 23.5 - - + +
406A GLY 5.2 0.5 - - - +
408A MET* 3.6 22.1 - - + +
413A ARG* 5.2 5.5 - - - +
416A LEU* 3.3 34.1 - - - +
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Residues in contact with MET 402 (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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398A ILE* 3.4 31.2 - - + +
399A THR* 2.9 23.1 + - + +
401A LYS* 1.3 84.0 - - - +
403A GLU* 1.3 65.4 + - + +
404A ILE 3.4 5.0 + - - +
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Residues in contact with GLU 403 (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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221A GLN* 3.2 53.7 + - + +
222A LEU* 3.8 19.1 - - + +
224A LEU* 4.8 1.4 - - - +
396A ARG* 2.8 39.5 + - - -
399A THR* 3.8 17.6 - - + +
400A LEU* 3.0 12.2 + - - +
402A MET* 1.3 79.5 - - + +
404A ILE* 1.3 59.6 + - - +
405A PRO* 3.9 4.5 - - - +
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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