Contacts of the helix formed by residues 103 - 109 (chain C) in PDB entry 4E3C
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 ASP 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C ARG 5.4 1.6 - - - +
21C LEU 4.6 12.8 - - - +
102C GLY* 1.3 73.8 - - - +
104C LEU* 1.3 52.6 - - - +
105C ARG* 2.4 22.8 + - + +
106C LYS* 2.5 30.9 + - + +
148C PRO 4.0 4.0 - - - -
149C GLU* 3.5 24.0 - - - +
151C ILE 4.2 2.0 - - - -
152C VAL* 3.6 17.5 - - - +
165C ILE* 6.4 0.2 - - - -
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Residues in contact with LEU 104 (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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102C GLY 3.3 1.4 - - - -
103C ASP* 1.3 72.0 - - - +
105C ARG* 1.3 50.9 + - - +
107C TYR* 2.6 32.3 + - + +
108C LEU* 2.9 32.8 + - + -
117C LEU* 6.4 0.7 - - + -
125C LEU* 4.3 15.5 - - + -
148C PRO* 3.1 41.3 + - + +
151C ILE* 3.0 31.5 + - + +
153C LEU* 3.7 29.2 - - + -
162C HIS* 4.7 9.0 - - + +
211C LEU* 4.6 1.8 - - + -
215C CYS* 4.5 9.9 - - - -
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Residues in contact with ARG 105 (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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103C ASP* 2.4 11.7 + - + +
104C LEU* 1.3 73.5 - - - +
106C LYS* 1.3 53.0 + - - +
108C LEU* 3.1 7.7 + - + +
109C ASN* 2.7 58.4 + - - +
148C PRO* 3.4 26.0 + - - +
149C GLU* 2.6 53.4 + - + +
185C THR* 4.8 10.3 + - - +
188C TYR* 2.8 27.0 + - - -
214C GLU* 3.0 22.6 + - - -
220C ARG* 3.7 13.1 - - - +
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Residues in contact with LYS 106 (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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102C GLY 4.0 13.1 - - - +
103C ASP* 2.5 26.2 + - + +
105C ARG* 1.3 74.3 - - - +
107C TYR* 1.3 63.5 + - + +
109C ASN* 3.8 6.7 + - - +
110C GLN* 3.1 39.3 + - - +
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Residues in contact with TYR 107 (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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102C GLY* 3.8 21.1 + - - -
104C LEU* 2.6 21.7 + - + +
106C LYS* 1.3 77.1 - - + +
108C LEU* 1.3 57.9 + - + +
109C ASN 3.0 1.6 - - - -
110C GLN* 2.7 44.7 + - + +
113C ASN* 3.3 13.8 + - - +
117C LEU* 6.0 1.6 - - + -
153C LEU* 3.5 50.1 + - + +
160C LEU* 3.8 19.1 - - + +
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Residues in contact with LEU 108 (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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104C LEU* 2.9 42.1 + - + +
105C ARG* 3.8 9.9 - - - +
107C TYR* 1.3 75.5 - - - +
109C ASN* 1.3 59.3 + - - +
110C GLN 3.4 8.0 + - - +
113C ASN* 4.2 16.5 - - - +
114C CYS* 5.1 1.9 - - - -
117C LEU* 4.2 16.2 - - + -
148C PRO* 3.9 19.3 - - + -
214C GLU* 4.0 28.3 - - + +
215C CYS* 4.0 38.1 - - - +
218C GLY* 6.2 0.2 - - - -
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Residues in contact with ASN 109 (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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105C ARG* 2.7 58.4 + - - +
106C LYS* 4.0 8.7 - - - +
108C LEU* 1.3 70.8 - - - +
110C GLN* 1.3 66.5 + - - +
111C PHE* 3.6 15.6 + - - -
427C ARG* 4.4 15.5 + - - +
575C ARG* 5.6 0.7 - - - -
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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