Contacts of the helix formed by residues 391 - 396 (chain A) in PDB entry 4L1O
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 ILE 391 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A TRP* 4.1 11.9 - - + -
234A GLY* 3.7 36.1 - - - +
237A MET* 4.5 9.9 - - + -
242A THR* 4.2 9.9 - - + -
244A VAL* 3.5 37.0 - - + +
245A ALA* 4.1 2.5 - - - +
364A TYR* 3.0 19.6 + - - -
390A VAL* 1.3 74.1 - - + +
392A VAL* 1.3 58.4 - - - +
393A HIS* 2.8 13.0 + - - -
394A ILE* 3.1 20.8 + - - +
395A THR* 4.3 1.1 - - + +
601A 1VL 3.6 39.3 - - - +
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Residues in contact with VAL 392 (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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233A TRP* 3.8 9.4 - - + -
386A ALA* 5.2 0.9 - - + -
389A ASP* 3.6 23.3 - - + +
390A VAL 2.6 17.9 + - - +
391A ILE* 1.3 72.9 - - - +
393A HIS* 1.3 61.5 + - + +
394A ILE 3.2 0.2 - - - -
395A THR* 2.8 30.1 + - - +
396A LEU* 3.6 9.8 - - + +
428B LEU* 3.3 28.3 - - + -
430B ARG* 3.9 9.6 - - - +
438B LEU* 5.8 0.2 - - + -
441B ARG* 3.4 27.8 - - - +
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Residues in contact with HIS 393 (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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244A VAL* 4.8 0.7 - - + -
361A LEU 5.2 0.9 - - - -
362A ALA* 3.8 12.5 - - + +
364A TYR* 3.4 27.0 + + - -
384A GLY* 4.1 26.8 - - - -
385A VAL 4.0 14.3 + - - +
386A ALA* 3.6 18.8 - - + +
391A ILE 2.8 12.7 + - - -
392A VAL* 1.3 77.0 - - - +
394A ILE* 1.3 79.5 + - + +
395A THR 3.2 1.8 + - - -
396A LEU* 3.8 11.9 + - - -
399A LEU* 3.9 25.8 - - + +
401A PHE* 5.5 1.1 - + - -
426B SER* 4.7 6.5 + - - +
428B LEU* 3.8 31.2 - - + -
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Residues in contact with ILE 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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243A CYS* 4.2 1.3 - - - -
244A VAL* 3.6 26.2 - - + -
391A ILE 3.1 13.6 + - - +
393A HIS* 1.3 103.4 - - + +
395A THR* 1.3 65.0 + - + +
396A LEU 3.6 0.9 - - - -
399A LEU 5.5 0.9 - - - -
401A PHE* 3.4 36.6 - - + -
413A HIS* 3.0 31.0 + - - -
601A 1VL 3.5 52.6 - - + +
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Residues in contact with THR 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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65A TYR* 3.8 38.8 + - + +
68A GLU* 5.2 3.8 - - - +
391A ILE* 4.3 4.0 - - + +
392A VAL* 2.8 25.3 + - - +
393A HIS 3.2 0.2 - - - -
394A ILE* 1.3 83.4 - - + +
396A LEU* 1.3 68.1 + - - +
397A HIS 3.8 2.3 + - - -
413A HIS* 5.0 3.4 - - - -
601A 1VL 3.5 32.5 - - - -
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Residues in contact with LEU 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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392A VAL* 3.6 17.5 - - + +
393A HIS* 3.8 5.3 + - - +
394A ILE 3.6 2.3 - - - -
395A THR* 1.3 86.0 - - - +
397A HIS* 1.3 67.6 + - - +
398A SER* 3.1 6.5 - - - +
399A LEU* 3.0 52.7 + - + +
413A HIS* 5.2 4.5 + - - +
89B THR* 4.6 13.0 - - + +
91B GLN* 6.3 0.7 - - + -
92B THR* 3.7 33.4 - - + -
97B LEU* 3.9 10.1 - - + -
428B LEU* 4.2 16.4 - - + -
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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