Contacts of the helix formed by residues 142 - 146 (chain F) in PDB entry 4CEV
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 142 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F HIS 3.5 26.0 - - - +
100F SER* 4.2 1.3 - - - -
102F ALA* 4.0 9.4 - - + -
103F ILE* 3.5 27.9 - - + +
120F TRP* 3.7 18.8 - - + -
126F ASP* 3.9 2.9 - - + +
138F ILE 3.2 12.7 - - - +
139F HIS* 3.3 15.5 - - - +
140F GLY 3.6 0.9 - - - -
141F MET 1.4 89.9 - - - +
143F LEU* 1.3 55.8 + - - +
145F ALA* 3.9 0.9 - - - +
146F SER* 2.7 37.1 + - - -
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Residues in contact with LEU 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F VAL* 4.9 0.9 - - + -
120F TRP* 3.8 44.8 - - + -
125F GLY 3.5 18.8 - - - +
126F ASP 3.0 13.7 + - - +
127F VAL* 3.7 12.6 - - + -
142F PRO* 1.3 77.4 - - - +
144F ALA* 1.3 66.3 + - - +
146F SER* 3.2 1.9 + - - -
147F LEU* 3.0 35.2 + - + +
164F ILE* 3.9 23.3 - - + -
169F VAL* 4.1 23.6 - - + -
171F LEU* 4.0 13.5 - - + -
190F ILE* 5.4 1.6 - - + -
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Residues in contact with ALA 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F ASP 3.4 2.2 + - - -
127F VAL* 3.5 32.8 - - - +
128F ASN 3.7 10.8 - - - +
129F THR* 4.7 0.9 - - + -
141F MET 3.3 1.9 + - - +
143F LEU* 1.3 78.0 - - - +
145F ALA* 1.3 61.7 + - - +
147F LEU* 2.9 11.7 + - - +
148F GLY 3.1 0.2 + - - -
149F PHE* 2.8 33.4 + - + +
184F PHE* 4.1 25.1 - - + -
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Residues in contact with ALA 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F ILE* 4.1 22.4 - - + -
141F MET* 3.0 19.0 + - + +
142F PRO 4.0 3.4 - - - +
144F ALA* 1.3 76.0 - - - +
146F SER* 1.3 57.8 + - - +
148F GLY* 3.0 18.5 + - - -
149F PHE 3.3 14.7 + - - +
150F GLY* 5.4 1.6 - - - -
154F LEU* 4.1 22.8 - - + +
155F THR* 3.6 20.6 - - + +
162F PRO* 5.7 0.2 - - - +
163F LYS* 5.4 1.2 - - - +
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Residues in contact with SER 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F ILE* 4.1 15.6 + - - +
106F LEU* 3.3 33.5 - - - +
142F PRO 2.7 23.1 + - - -
143F LEU 3.6 4.9 - - - -
144F ALA 3.1 0.2 - - - -
145F ALA* 1.3 72.6 - - - +
147F LEU* 1.3 56.0 + - - +
148F GLY 3.0 6.3 + - - -
163F LYS* 2.9 42.3 + - - +
164F ILE* 3.4 15.3 + - - -
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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