Contacts of the helix formed by residues 141 - 146 (chain C) in PDB entry 3FTN
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 141 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C GLU 3.6 8.3 - - - +
140C ILE* 1.3 90.2 - - + +
142C LEU* 1.3 60.2 + - - +
143C GLU* 3.9 14.8 - - + +
144C ALA* 3.2 15.1 + - + +
145C ALA* 2.8 25.6 + - - +
309C VAL* 6.0 1.1 - - + -
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Residues in contact with LEU 142 (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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32C LEU* 4.4 28.9 - - + +
33C ALA* 4.2 13.1 - - + +
62C VAL* 3.7 32.5 - - + +
80C ARG* 4.2 23.6 - - - +
136C LEU* 4.1 12.6 - - + -
140C ILE 3.6 1.6 + - - -
141C PRO* 1.3 70.9 - - - +
143C GLU* 1.3 72.4 + - - +
145C ALA* 3.1 5.2 + - - +
146C VAL* 2.9 26.9 + - - +
350C ILE* 5.0 15.7 - - + -
352C ALA* 5.3 6.5 - - + +
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Residues in contact with GLU 143 (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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141C PRO* 3.9 11.7 - - + +
142C LEU* 1.3 85.9 + - - +
144C ALA* 1.3 62.7 + - - +
146C VAL* 3.4 17.5 - - - +
147C MET* 3.7 10.0 - - - +
317C SER* 5.6 4.5 - - - -
320C VAL* 3.8 17.8 - - + +
323C VAL* 4.2 28.9 - - + +
348C VAL* 4.4 15.9 - - + -
350C ILE* 3.2 26.7 - - + +
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Residues in contact with ALA 144 (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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140C ILE* 4.4 5.8 - - + -
141C PRO* 3.2 25.8 + - + +
143C GLU* 1.3 79.4 - - - +
145C ALA* 1.3 66.3 + - - +
147C MET* 3.0 23.9 + - - +
148C ILE* 3.9 4.3 + - - +
309C VAL* 5.3 2.5 - - + -
315C ASP* 5.2 1.1 - - - +
316C PRO* 4.0 27.2 - - + +
317C SER* 4.4 18.8 - - - +
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Residues in contact with ALA 145 (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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62C VAL* 3.6 19.7 - - + +
82C VAL* 4.5 4.6 - - + +
136C LEU* 3.7 28.0 - - + -
140C ILE* 3.9 3.8 - - + +
141C PRO 2.8 17.6 + - - +
142C LEU* 3.5 8.1 - - - +
144C ALA* 1.3 77.1 - - - +
146C VAL* 1.3 56.3 + - - +
148C ILE* 2.9 39.9 + - + +
149C PRO* 3.4 4.2 - - - +
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Residues in contact with VAL 146 (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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33C ALA* 3.6 26.9 - - + +
34C VAL* 3.9 8.5 - - - -
35C ALA* 4.2 3.1 - - + +
60C GLU* 3.8 28.1 - - - +
61C ALA* 3.9 9.6 - - - +
62C VAL* 3.9 9.0 - - + +
142C LEU 2.9 13.8 + - - +
143C GLU 3.4 10.5 - - - +
144C ALA 3.2 0.4 - - - -
145C ALA* 1.3 75.5 - - - +
147C MET* 1.3 67.2 + - + +
148C ILE 3.3 0.4 - - - -
149C PRO* 3.1 15.9 - - - +
348C VAL* 3.4 37.5 - - + -
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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