Contacts of the helix formed by residues 298 - 303 (chain C) 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 PRO 298 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C THR* 3.3 28.0 - - + +
186C TYR* 4.0 18.6 - - + +
188C THR* 4.4 4.5 - - - -
294C ASN 3.7 10.8 - - - +
295C THR 3.8 11.6 - - - +
296C VAL 3.6 2.9 - - - -
297C TYR* 1.3 87.2 - - - +
299C SER* 1.3 60.8 + - - +
300C GLU* 3.6 15.0 - - - +
301C PHE* 3.1 26.5 + - + -
302C TYR* 3.0 29.9 + - + +
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Residues in contact with SER 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C TYR* 3.4 6.6 - - - -
188C THR* 4.9 1.3 + - - -
294C ASN* 3.6 11.2 + - - +
297C TYR 3.4 0.4 + - - -
298C PRO* 1.3 68.0 - - - +
300C GLU* 1.3 66.9 + - - +
301C PHE 3.1 2.2 - - - -
303C GLY* 3.0 40.4 + - - -
308C GLU* 2.7 28.4 + - - -
395C TYR* 3.4 24.5 + - - -
423C ARG* 3.1 14.5 + - - +
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Residues in contact with GLU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C MET* 4.9 5.0 + - - +
82C TYR* 3.4 17.4 - - - -
102C GLY* 3.6 20.9 - - - +
186C TYR* 2.7 33.3 + - + +
188C THR* 2.8 31.6 + - - +
194C GLY* 4.1 5.0 + - - -
298C PRO* 3.6 4.9 - - + +
299C SER* 1.3 86.7 + - - +
301C PHE* 1.3 75.5 + - + +
364C PRO* 5.4 0.3 - - - +
391C ARG* 5.3 11.8 + - - +
395C TYR* 3.7 11.2 + - - +
526C DMS 3.6 16.2 + - - +
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Residues in contact with PHE 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C MET* 3.6 40.9 - - + +
82C TYR* 3.7 10.4 + - - +
90C PRO* 3.8 25.1 - - + +
93C ALA* 3.7 26.0 - - + -
94C THR* 3.6 24.9 - - - -
99C VAL* 4.1 6.7 - - + -
103C GLY* 3.5 32.3 - - - -
186C TYR* 3.7 44.0 - + - -
298C PRO* 3.1 18.2 + - + +
300C GLU* 1.3 85.1 - - + +
302C TYR* 1.3 62.6 + - + +
303C GLY 3.5 0.9 - - - -
422C PRO* 4.6 1.2 - - - +
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Residues in contact with TYR 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TYR* 3.7 4.5 - - - -
87C ILE* 4.3 2.7 - - - -
90C PRO* 3.6 22.2 - - + -
91C HIS* 3.1 43.1 + + - -
94C THR* 3.7 17.4 + - - -
290C VAL* 4.7 2.9 - - + -
296C VAL 4.4 1.7 + - - -
297C TYR* 3.5 40.9 - + + -
298C PRO* 3.0 24.7 + - + +
301C PHE* 1.3 79.1 - - + +
303C GLY* 1.3 60.4 + - - +
421C SER* 3.5 6.9 + - - -
422C PRO* 3.4 31.2 - - + +
423C ARG* 3.6 25.2 - - + +
426C LEU* 3.8 30.7 - - + -
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Residues in contact with GLY 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TYR* 3.3 21.7 - - - -
299C SER* 3.0 20.3 + - - -
302C TYR* 1.3 75.7 - - - +
304C PRO* 1.3 69.0 - - - +
398C HIS 5.3 0.4 - - - -
419C PHE* 6.0 0.4 - - - -
421C SER* 4.8 3.1 - - - -
423C ARG* 2.6 34.5 + - - -
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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