Contacts of the helix formed by residues 133 - 137 (chain V) in PDB entry 4IL6
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 133 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104U LYS* 4.4 9.0 - - - -
43V GLY 5.2 1.2 + - - -
45V ILE* 3.5 20.2 - - - +
129V LYS 4.3 3.5 + - - +
131V GLY 3.5 2.4 - - - -
132V GLY* 1.3 79.2 - - - +
134V LYS* 1.3 66.7 + - - -
135V VAL 3.2 0.4 - - - -
136V TYR* 3.0 16.5 + - - +
137V TYR* 3.4 23.7 - - - -
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Residues in contact with LYS 134 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ARG* 3.4 8.8 + - - -
326A LEU* 3.6 25.8 - - + +
329A GLU* 2.7 29.7 + - - +
330A VAL* 3.9 12.8 - - + -
340A PRO 4.4 11.4 + - - -
412C THR* 5.7 0.2 - - - -
328D TRP* 3.8 6.4 - - + -
348D ARG* 3.6 15.5 - - - +
351D ALA 5.3 0.2 + - - -
352D LEU* 2.8 38.3 + - - +
104U LYS* 4.8 6.9 + - - +
133V GLY* 1.3 68.2 - - - -
135V VAL* 1.3 67.9 + - + +
136V TYR 3.0 1.0 + - - -
137V TYR* 3.1 36.1 + - + +
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Residues in contact with VAL 135 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ARG* 2.9 21.0 + - - -
328D TRP* 3.7 19.7 - - + -
343D GLU* 3.9 25.8 - - + +
346D LEU* 4.0 17.9 - - + -
348D ARG* 3.5 28.3 - - - +
416D DMS 4.1 13.0 - - - +
104U LYS* 4.2 7.4 - - - +
132V GLY 4.5 3.4 - - - +
133V GLY 3.1 1.0 + - - -
134V LYS* 1.3 77.5 - - - +
136V TYR* 1.3 82.0 + - + +
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Residues in contact with TYR 136 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A ARG* 4.1 0.2 - - - -
332D GLN* 5.2 0.7 - - - +
343D GLU* 3.6 21.2 + - - +
416D DMS 4.4 23.9 + - - +
55V ARG* 4.2 4.5 - - - -
128V ASP* 3.7 33.2 + - + +
129V LYS* 3.3 45.7 + - + +
132V GLY* 3.6 28.5 - - - -
133V GLY 3.0 8.8 + - - +
135V VAL* 1.3 89.1 - - + +
137V TYR* 1.3 69.3 + - + +
206V GOL 3.4 27.5 + - - -
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Residues in contact with TYR 137 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A HIS* 2.6 31.9 + + - -
315A ASN* 4.7 7.4 + - - -
319A ASP* 4.9 3.8 - - - +
322A ASN* 4.1 10.9 + - - +
323A ARG* 3.0 30.3 + - - -
326A LEU* 3.9 15.9 - - + -
412C THR* 3.3 28.5 - - - -
413C GLU* 4.4 16.2 + - - -
414C ILE* 3.6 41.8 + - + +
332D GLN* 3.5 10.4 + - - +
42V VAL* 5.4 6.2 + - - +
43V GLY* 6.1 1.8 - - - -
45V ILE* 5.2 7.6 - - - +
47V LYS* 6.1 0.7 - - - -
129V LYS* 4.2 5.1 + - - -
133V GLY* 3.4 25.7 - - - -
134V LYS* 3.1 37.1 + - + +
136V TYR* 1.3 82.7 - - + +
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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