Contacts of the helix formed by residues 177 - 180 (chain B) in PDB entry 1FFT
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 177 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409A VAL* 4.0 2.2 - - + +
476A PHE 5.2 0.2 - - - +
477A MET 4.0 17.3 - - - +
478A GLY* 4.2 19.5 - - - +
32B PRO* 3.6 15.3 - - + +
175B PHE* 3.7 33.6 - - + +
176B ILE* 1.3 78.8 - - + +
178B ARG* 1.3 61.5 + - - +
179B LEU 2.4 17.8 + - - -
180B GLY* 2.5 16.3 + - - -
204B ASP 3.4 18.4 - - - +
205B GLY* 4.7 1.3 - - - -
206B ILE* 4.4 8.7 - - + +
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Residues in contact with ARG 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476A PHE 3.4 13.9 + - - -
477A MET* 3.7 16.5 - - - +
490A GLN* 6.0 0.4 + - - +
28B ALA* 4.7 14.8 - - - +
30B LEU 4.5 5.3 + - - -
31B ASP 4.3 4.2 + - - -
32B PRO* 2.9 47.9 - - - +
33B LYS* 3.4 53.9 - - + +
35B GLN* 5.0 1.9 + - - +
36B ILE* 3.5 15.6 - - - +
39B GLU* 3.9 1.3 - - - +
43B LEU* 5.7 0.4 - - - -
176B ILE* 3.7 2.3 - - + +
177B PRO* 1.3 80.3 - - - +
179B LEU* 1.3 60.2 + - + +
180B GLY 3.7 0.2 - - - -
203B TYR* 4.4 25.2 - - + -
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B GLN* 4.4 8.1 - - + +
36B ILE* 3.1 51.3 - - + +
38B LEU* 5.8 0.3 - - - +
39B GLU* 5.0 2.0 - - - -
155B PHE* 5.5 4.9 - - + -
176B ILE* 3.2 33.2 - - + +
177B PRO 2.4 17.6 + - - -
178B ARG* 1.3 73.9 - - - +
180B GLY* 1.3 66.2 + - - +
181B SER* 3.1 16.8 + - - +
195B LEU* 3.7 31.4 - - + +
196B ILE 4.5 1.1 - - - +
197B ALA* 4.6 9.9 - - + -
203B TYR* 5.0 22.9 - - + -
222B ALA* 5.1 4.9 - - + -
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Residues in contact with GLY 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A PHE* 5.3 2.6 - - - +
409A VAL* 3.4 37.6 - - - +
36B ILE* 5.1 1.3 - - - +
38B LEU* 5.8 2.1 - - - +
39B GLU* 5.6 1.6 - - - -
42B SER* 4.9 7.8 + - - -
43B LEU* 5.1 9.0 - - - +
114B LEU* 4.2 13.9 - - - +
175B PHE* 3.9 2.7 - - - -
176B ILE 2.8 3.0 + - - -
177B PRO 2.5 15.9 + - - -
178B ARG 3.7 0.4 - - - -
179B LEU* 1.3 71.9 - - - +
181B SER* 1.3 56.5 + - - -
182B GLN 4.0 1.6 + - - -
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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