Contacts of the helix formed by residues 56 - 61 (chain G) in PDB entry 1IB1
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 PHE 56 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52G GLU* 2.8 44.0 + - + +
55G ALA* 1.3 77.7 - - + +
57G ILE* 1.3 67.5 + - - +
58G SER 3.1 2.0 - - - -
59G VAL* 2.9 14.8 + - - +
60G SER* 3.1 15.5 + - - -
62G ASN 3.2 14.3 - - - +
63G CYS* 3.7 7.0 - - + -
64G PRO* 3.6 17.9 - - + -
93G PHE* 4.7 2.0 - + - -
123G ALA* 5.1 0.4 - - + -
124G LEU 3.6 23.8 - - - -
125G ALA* 3.7 19.7 - - + -
402G COT 3.2 73.4 - + + -
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Residues in contact with ILE 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G PHE* 3.5 36.6 - - + -
52G GLU 3.0 4.8 + - - +
53G ARG* 3.6 24.9 - - + +
56G PHE* 1.3 74.4 - - - +
58G SER* 1.3 57.2 - - - +
61G GLY* 2.9 39.6 + - - +
62G ASN 3.4 10.1 - - - +
63G CYS* 3.6 22.9 - - + -
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Residues in contact with SER 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G ARG 3.0 9.7 + - - -
54G GLU* 2.6 28.6 + - - -
56G PHE 3.0 0.4 + - - -
57G ILE* 1.3 77.1 - - - +
59G VAL* 1.3 69.4 + - - +
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Residues in contact with VAL 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G GLU 5.0 0.2 - - - +
55G ALA 3.7 19.7 - - - +
56G PHE* 2.9 5.1 + - - +
58G SER* 1.3 89.4 - - - +
60G SER* 1.3 65.7 + - - +
61G GLY 3.6 0.4 - - - -
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Residues in contact with SER 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G PHE* 3.1 7.6 + - - -
59G VAL* 1.3 80.8 - - - +
61G GLY* 1.3 59.6 + - - +
62G ASN* 3.1 12.9 + - - -
161G GLU* 5.7 0.8 + - - -
186G LEU* 3.5 31.4 - - - +
402G COT 3.3 25.3 - - - -
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Residues in contact with GLY 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G ILE* 2.9 34.6 + - - +
59G VAL 3.6 0.8 - - - -
60G SER* 1.3 77.0 - - - +
62G ASN* 1.3 63.4 + - - +
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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