Contacts of the helix formed by residues 53 - 58 (chain C) in PDB entry 2GTL
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 LEU 53 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49C GLU 3.5 18.6 - - - +
50C VAL* 2.6 19.7 + - + +
52C ASP* 1.3 71.8 - - + +
54C PHE* 1.3 61.1 + - + +
55C LYS 3.1 7.7 + - - -
56C ARG* 4.0 12.5 + - - +
105C ARG* 4.4 6.9 + - - -
106C GLU 3.6 10.8 - - - +
107C GLY* 3.5 32.8 - - - +
108C VAL* 4.0 4.5 - - + +
112C HIS* 3.6 30.5 - - + -
160C HEM 3.9 39.4 - - + +
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Residues in contact with PHE 54 (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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40C LEU* 3.5 32.8 - - + -
43C LEU* 4.7 2.0 - - + -
50C VAL* 3.1 33.3 + - + +
53C LEU* 1.3 74.4 - - + +
55C LYS* 1.3 63.8 + - - +
56C ARG 3.2 2.5 - - - -
57C VAL* 3.0 26.9 + - + +
59C ILE* 3.2 44.9 + - + -
67C PHE* 4.8 0.7 - + - -
70C HIS* 3.5 22.0 - + - -
160C HEM 3.4 59.2 - + + -
161C CMO 3.7 10.8 - - - -
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Residues in contact with LYS 55 (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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51C ASN 3.2 12.2 + - - +
52C ASP* 3.0 35.4 - - + +
53C LEU 3.1 0.6 - - - -
54C PHE* 1.3 78.1 - - - +
56C ARG* 1.3 58.1 + - - +
58C ASP* 2.9 22.3 + - - -
59C ILE* 4.3 5.2 - - - -
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Residues in contact with ARG 56 (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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91B HIS* 4.9 20.4 + - - +
94B VAL* 6.2 2.0 - - - +
53C LEU 4.0 5.1 + - - +
55C LYS* 1.3 80.3 - - - +
57C VAL* 1.3 61.8 + - - +
58C ASP 3.6 1.6 + - - -
66C LYS* 5.1 9.2 + - - +
73C ARG* 4.8 5.7 - - - +
105C ARG* 4.0 23.7 - - - +
160C HEM 3.4 37.2 + - - +
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Residues in contact with VAL 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C PHE* 3.0 29.4 - - + +
56C ARG* 1.3 83.2 - - - +
58C ASP* 1.3 69.9 + - - +
66C LYS* 4.2 12.1 - - - +
67C PHE* 3.3 38.3 + - + -
70C HIS* 4.0 24.9 - - + +
73C ARG* 4.0 9.4 - - - +
160C HEM 3.3 34.5 - - - +
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Residues in contact with ASP 58 (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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55C LYS* 2.9 14.6 + - - +
56C ARG 3.3 2.0 + - - -
57C VAL* 1.3 81.0 - - - +
59C ILE* 1.3 60.7 + - - +
60C GLU* 2.9 14.2 - - - +
61C HIS* 2.9 57.4 + - - +
64C GLY* 4.4 3.8 - - - -
66C LYS* 3.6 27.1 - - + +
67C PHE* 3.6 2.3 - - - +
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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