Contacts of the helix formed by residues 16 - 21 (chain L) in PDB entry 2I2X
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 TYR 16 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74I VAL* 3.2 39.7 - - + +
77I GLY* 3.7 9.4 - - - -
78I PHE 2.5 29.8 + - - -
79I PRO* 3.5 9.2 - - - +
116I TYR* 3.3 49.8 - + + -
117I GLY 4.9 0.9 - - - -
118I ILE* 3.4 22.8 - - + +
233K LEU* 4.3 3.4 - - + +
234K LEU* 3.9 11.0 - - + -
14L THR* 3.0 50.1 + - + -
15L ARG* 1.3 71.7 - - - +
17L ASN* 1.3 62.2 + - - +
18L VAL 3.2 0.5 + - - -
19L ALA* 3.8 6.3 + - - +
20L LEU* 3.7 22.2 + - - +
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Residues in contact with ASN 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233K LEU* 3.3 38.9 - - - +
234K LEU* 3.6 16.3 - - + +
415K SER* 4.0 10.4 + - - -
418K GLU* 3.6 28.4 - - - +
15L ARG* 3.4 31.4 + - - +
16L TYR* 1.3 73.8 - - - +
18L VAL* 1.3 68.1 + - - +
20L LEU* 3.5 4.4 + - - +
21L GLU* 3.5 18.9 + - - +
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Residues in contact with VAL 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413K GLU* 3.5 55.6 - - + +
414K LEU 4.6 6.3 - - - +
415K SER* 4.2 17.0 - - - +
416K ARG* 5.5 0.7 + - - -
15L ARG* 2.9 30.5 + - + +
17L ASN* 1.3 84.6 - - - +
19L ALA* 1.3 63.4 + - - +
20L LEU 3.3 0.3 + - - -
21L GLU* 3.3 15.8 + - - +
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Residues in contact with ALA 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L ARG 4.4 1.4 + - - -
16L TYR 3.8 6.3 + - - +
17L ASN 3.6 0.2 - - - -
18L VAL* 1.3 80.2 - - - +
20L LEU* 1.3 63.2 + - + +
21L GLU 3.4 5.5 + - - +
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Residues in contact with LEU 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115I GLU* 3.9 34.8 - - + +
116I TYR* 3.5 34.3 - - + +
234K LEU* 4.0 15.9 - - + -
16L TYR 3.7 10.7 + - - +
17L ASN* 3.5 5.3 + - - +
18L VAL 3.3 1.4 - - - -
19L ALA* 1.3 78.8 - - + +
21L GLU* 1.3 64.8 + - - +
22L LYS* 3.3 7.6 + - - +
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Residues in contact with GLU 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415K SER* 3.8 10.2 - - - -
416K ARG* 2.9 54.9 + - - +
417K PHE* 2.9 34.5 + - - +
17L ASN 3.5 8.9 + - - +
18L VAL 3.3 14.1 + - - +
19L ALA 3.2 7.9 - - - +
20L LEU* 1.3 78.3 - - - +
22L LYS* 1.3 74.6 + - - +
23L ALA 3.8 0.5 + - - -
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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