Contacts of the helix formed by residues 167 - 174 (chain B) in PDB entry 5FLM
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 THR 167 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B GLY 3.9 1.8 + - - -
166B LEU* 1.3 76.3 - - - +
168B ASP* 1.3 74.5 + - - +
169B ARG* 4.1 13.2 - - + +
170B ASP* 3.5 19.6 + - - +
171B LEU* 3.1 24.5 + - - +
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Residues in contact with ASP 168 (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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167B THR* 1.3 84.3 + - - +
169B ARG* 1.3 68.1 + - + +
171B LEU* 3.1 5.6 + - - +
172B CYS* 2.9 32.4 + - - -
178B PRO* 3.1 32.8 - - + +
58J LYS* 5.8 1.6 + - - -
61J ASN* 4.7 8.0 + - - -
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Residues in contact with ARG 169 (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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167B THR* 3.5 8.1 - - + +
168B ASP* 1.3 79.8 - - + +
170B ASP* 1.3 62.2 + - - +
172B CYS* 3.1 9.5 + - - +
173B GLU* 2.9 38.2 + - + +
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Residues in contact with ASP 170 (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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166B LEU* 3.7 34.0 - - + +
167B THR* 3.5 24.0 + - - +
168B ASP 3.2 0.4 - - - -
169B ARG* 1.3 79.8 - - - +
171B LEU* 1.3 62.5 + - - +
173B GLU* 3.2 19.6 + - - +
174B LEU* 3.0 33.1 + - + +
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Residues in contact with LEU 171 (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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157B ARG* 5.4 9.2 - - - +
163B LEU* 3.9 37.0 - - + +
166B LEU* 3.9 29.2 - - + +
167B THR 3.1 17.5 + - - +
168B ASP 3.1 7.6 + - - +
170B ASP* 1.3 77.2 - - - +
172B CYS* 1.3 56.3 + - - +
174B LEU* 3.5 2.9 + - - -
175B ASN 3.2 4.5 + - - -
176B GLU* 2.8 48.1 + - + +
177B CYS 4.9 2.5 - - - +
178B PRO* 4.2 27.6 - - + +
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Residues in contact with CYS 172 (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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168B ASP* 2.9 36.2 + - - -
169B ARG* 3.1 11.2 + - - +
171B LEU* 1.3 75.9 - - - +
173B GLU* 1.3 64.6 + - + +
174B LEU 3.1 1.8 - - - -
175B ASN* 3.2 14.0 + - - +
178B PRO* 4.6 6.3 - - - -
61J ASN* 3.7 37.9 - - + +
62J TYR* 3.4 37.2 - - + -
63J ALA 5.1 1.2 + - - -
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Residues in contact with GLU 173 (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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169B ARG* 2.9 22.4 + - - +
170B ASP* 3.6 21.4 - - - +
172B CYS* 1.3 75.9 - - + +
174B LEU* 1.3 64.9 + - + +
175B ASN* 3.3 6.9 + - - +
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Residues in contact with LEU 174 (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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109B MET* 3.5 52.7 - - + +
111B ASN* 4.2 7.8 + - - +
163B LEU* 4.4 2.9 - - + -
166B LEU* 3.6 26.7 - - + -
170B ASP* 3.0 20.9 + - + +
171B LEU* 3.5 6.3 + - - +
172B CYS 3.1 0.4 - - - -
173B GLU* 1.3 81.4 - - + +
175B ASN* 1.3 70.2 + - - +
176B GLU* 3.3 15.7 + - + +
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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