Contacts of the helix formed by residues 173 - 177 (chain C) 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 HIS 173 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802B ASP* 2.9 56.7 + - + +
807B ARG* 4.3 1.6 + - - -
66C HIS* 5.1 1.3 - + - -
70C LEU* 4.6 3.8 - - + -
170C GLY* 3.8 9.7 - - - +
171C LYS 3.6 0.2 - - - -
172C GLU* 1.3 80.5 - - - +
174C ALA* 1.3 58.0 + - - +
175C LYS* 3.0 45.1 + - + +
176C TRP* 3.0 38.9 + - + +
57L ALA 5.1 1.3 - - - -
58L ARG* 3.5 51.9 + - + +
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Residues in contact with ALA 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799B SER* 3.3 36.8 - - - +
802B ASP* 3.5 16.6 + - + +
803B ARG* 4.2 13.4 + - + +
70C LEU* 5.0 1.8 - - - -
170C GLY 4.5 2.6 + - - -
173C HIS* 1.3 75.7 + - - +
175C LYS* 1.3 61.6 + - - +
176C TRP 3.1 0.4 - - - -
177C ASN* 3.2 38.2 + - - +
6J ARG* 3.8 6.6 + - - -
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Residues in contact with LYS 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ILE* 5.0 2.3 - - - +
46C ALA* 3.7 13.3 - - + +
47C ILE 2.7 24.5 + - - +
48C ASP* 3.4 17.6 + - - +
69C GLY* 3.3 29.1 - - - +
70C LEU* 3.7 16.3 - - + +
173C HIS* 3.0 23.1 + - + +
174C ALA* 1.3 77.0 - - - +
176C TRP* 1.3 94.8 + - + +
177C ASN 3.3 1.3 - - - +
6J ARG* 3.3 27.9 + - - +
57L ALA* 3.3 18.5 - - - +
58L ARG* 3.7 16.2 - - - +
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Residues in contact with TRP 176 (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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42C VAL 4.2 1.0 - - - +
44C ILE* 3.0 35.8 - - + +
46C ALA* 3.8 24.6 + - + +
48C ASP* 4.3 21.1 - - + -
166C LYS* 4.1 7.7 + - + -
167C LYS 5.1 0.2 - - - -
168C GLY* 3.2 41.3 - - - +
169C PHE 3.4 18.2 - - - -
170C GLY* 3.8 8.2 + - - -
172C GLU* 3.5 26.0 - - + -
173C HIS* 3.0 40.5 + - + +
175C LYS* 1.3 104.0 - - + +
177C ASN* 1.3 61.6 + - - +
178C PRO* 3.2 7.3 - - - +
58L ARG* 3.8 20.6 - - - -
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Residues in contact with ASN 177 (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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799B SER* 4.4 5.3 + - - -
803B ARG* 3.2 26.8 - - - +
951B GLN* 3.6 11.3 + - - -
39C ILE* 3.5 25.3 - - + +
44C ILE* 4.2 3.9 - - - +
170C GLY* 3.4 21.2 + - - +
174C ALA* 3.2 26.3 + - - +
175C LYS 3.3 0.4 - - - -
176C TRP* 1.3 76.7 - - - +
178C PRO* 1.3 68.0 - - + +
179C THR* 3.3 15.5 + - + +
236C CYS* 4.5 2.8 - - - +
6J ARG* 4.1 17.6 + - - +
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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