Contacts of the helix formed by residues 100 - 105 (chain X) in PDB entry 3F6B
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 100 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99X GLN* 1.3 84.2 + - - +
101X ARG* 1.3 67.1 + - - +
102X ALA* 3.1 9.1 + - + +
103X MET* 2.8 44.7 + - + +
104X ILE* 3.4 7.6 + - - +
160X TYR* 3.5 36.3 - - - +
161X ASP* 3.0 30.3 + - - +
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Residues in contact with ARG 101 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99X GLN 3.5 0.4 + - - -
100X THR* 1.3 73.4 + - - +
102X ALA* 1.3 61.3 + - - +
103X MET 3.2 1.2 + - - -
104X ILE* 3.5 24.7 + - + +
105X GLY 4.6 1.6 + - - -
128X GLU* 5.0 3.6 + - - -
129X PRO* 3.0 31.1 + - - +
130X ALA* 3.5 14.5 + - - +
131X SER* 3.5 21.3 + - - +
132X ALA* 4.2 4.4 - - - +
159X PRO* 3.6 27.6 - - + +
161X ASP* 2.9 22.0 + - - +
162X ASP* 2.8 39.0 + - - -
165X LYS* 6.1 2.2 - - - +
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Residues in contact with ALA 102 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100X THR* 3.1 8.9 + - + +
101X ARG* 1.3 78.2 - - - +
103X MET* 1.3 70.1 + - + +
104X ILE 3.7 0.2 - - - -
105X GLY 5.0 1.8 + - - -
106X VAL* 5.4 5.0 - - - +
161X ASP* 4.7 1.6 + - - +
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Residues in contact with MET 103 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99X GLN* 3.6 22.9 - - - +
100X THR* 2.8 24.7 + - + +
102X ALA* 1.3 88.9 - - + +
104X ILE* 1.3 62.2 + - - +
105X GLY 3.4 2.5 - - - -
106X VAL* 3.5 20.7 - - + +
108X ALA* 3.3 43.6 + - + +
111X THR* 3.8 1.8 + - - -
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Residues in contact with ILE 104 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98X GLN* 3.6 32.3 - - + +
99X GLN* 3.7 18.8 - - + +
100X THR 3.5 9.6 - - - +
101X ARG* 3.5 23.2 + - + +
103X MET* 1.3 74.0 - - - +
105X GLY* 1.3 68.6 + - - +
107X GLU* 3.0 20.4 + - - +
111X THR* 4.1 16.6 - - + +
128X GLU* 4.2 12.6 - - - +
159X PRO* 4.3 5.6 - - + -
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Residues in contact with GLY 105 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101X ARG 4.6 2.6 + - - -
102X ALA 5.0 2.2 + - - -
103X MET 3.4 1.0 - - - -
104X ILE* 1.3 81.7 - - - +
106X VAL* 1.3 60.4 + - - +
107X GLU* 3.3 7.4 + - - +
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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