Contacts of the helix formed by residues 389 - 396 (chain B) in PDB entry 5IL2
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 389 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B LEU* 5.5 0.3 - - - +
159B LEU* 5.2 9.9 - - + -
388B CYS* 1.3 78.8 - - - +
390B GLU* 1.3 64.7 + - - +
391B GLU* 3.6 19.2 + - - +
392B ILE* 3.1 36.3 + - + +
393B GLU* 3.0 26.5 + - - +
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Residues in contact with GLU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B THR* 1.3 73.9 - - - +
391B GLU* 1.3 81.7 + - - +
393B GLU* 3.3 9.2 + - - +
394B ARG* 2.8 64.4 + - + +
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Residues in contact with GLU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B LEU* 4.1 20.9 - - + +
389B THR* 3.6 18.1 - - - +
390B GLU* 1.3 101.9 - - - +
392B ILE* 1.3 62.9 + - - +
394B ARG* 3.2 16.8 + - - +
395B LEU* 3.2 29.3 + - + +
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Residues in contact with ILE 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU* 4.2 9.2 - - + -
155B LEU* 3.6 46.9 - - + +
156B LYS* 3.8 21.5 - - + +
159B LEU* 3.8 26.5 - - + -
306B HIS* 3.8 11.7 - - + +
388B CYS* 3.6 17.9 - - - -
389B THR* 3.1 24.2 + - + +
391B GLU* 1.3 75.5 - - - +
393B GLU* 1.3 63.7 + - - +
395B LEU* 3.1 5.6 + - - +
396B ARG* 2.9 25.4 + - - +
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Residues in contact with GLU 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B GLY 4.7 8.0 - - - +
388B CYS* 3.8 22.8 - - + +
389B THR 3.0 20.5 + - - +
390B GLU* 3.3 11.9 + - - +
392B ILE* 1.3 77.3 - - - +
394B ARG* 1.3 62.7 + - + +
395B LEU 3.6 0.2 + - - -
396B ARG* 2.9 31.1 + - - +
398B LYS* 2.8 51.5 + - - +
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Residues in contact with ARG 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B GLU* 2.8 60.6 + - - +
391B GLU* 3.8 18.9 - - - +
392B ILE 3.2 0.6 - - - -
393B GLU* 1.3 77.9 - - + +
395B LEU* 1.3 63.3 + - + +
396B ARG 5.0 1.2 - - - +
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Residues in contact with LEU 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B LYS* 4.1 46.0 - - + +
151B GLU* 4.0 16.2 - - + -
152B LEU* 3.9 32.9 - - + +
155B LEU* 3.8 25.6 - - + -
391B GLU* 3.2 19.9 + - + +
392B ILE* 3.1 3.3 + - - +
394B ARG* 1.3 80.8 - - + +
396B ARG* 1.4 65.4 + - - +
397B PRO* 3.8 1.2 - - - +
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Residues in contact with ARG 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU* 3.9 14.1 - - + -
298B ARG* 5.6 4.0 + - - +
302B GLY* 3.7 25.1 + - - -
305B ILE 4.1 2.2 + - - -
306B HIS* 3.4 56.2 + - - +
307B ALA 4.5 3.4 + - - +
309B VAL* 5.0 4.0 - - + -
392B ILE* 2.9 18.4 + - + +
393B GLU* 2.9 29.9 + - - +
394B ARG 3.7 1.3 - - - +
395B LEU* 1.4 79.5 - - - +
397B PRO* 1.3 87.6 + - + +
398B LYS* 3.4 32.0 + - - +
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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