Contacts of the helix formed by residues 122 - 129 (chain D) in PDB entry 3FCS
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 TYR 122 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121D SER* 1.3 74.7 - - - +
123D SER* 1.3 58.6 + - - +
124D MET 3.1 5.6 + - - -
125D LYS* 3.3 42.5 + - + +
177D CYS* 4.1 27.1 - - + -
180D MET* 3.4 38.9 - - + +
182D THR* 5.1 10.9 + - + -
184D CYS* 5.7 0.4 - - + -
212D VAL* 4.2 13.7 - - + -
213D SER 2.8 14.1 + - - +
214D ARG* 4.5 18.3 - - + +
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Residues in contact with SER 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D SER* 2.9 9.3 + - - -
122D TYR* 1.3 79.9 - - - +
124D MET* 1.3 52.8 + - - +
125D LYS 3.4 2.2 - - - -
126D ASP* 3.5 1.8 - - - +
251D ASP* 2.5 33.8 + - - +
2002D CA 2.5 30.0 - - - -
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Residues in contact with MET 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D MET* 4.0 13.3 - - + +
119D ASP* 3.3 55.4 - - + +
120D LEU* 4.3 3.3 - - + +
121D SER* 2.9 12.7 + - - +
123D SER* 1.3 83.5 - - - +
125D LYS* 1.3 63.5 + - - +
126D ASP 3.4 1.6 - - - -
127D ASP* 3.1 47.6 + - + +
128D LEU* 3.4 9.2 + - - +
212D VAL* 3.8 8.1 - - - +
249D THR* 4.2 13.9 - - - +
250D THR* 4.4 5.6 - - - -
251D ASP* 3.8 31.4 - - - +
311D THR* 6.2 0.2 - - - -
333D LEU* 5.3 2.7 - - + -
335D MET 5.7 0.4 - - - +
337D SER* 4.5 2.2 - - - +
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Residues in contact with LYS 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D TYR* 3.3 36.5 + - + +
123D SER 3.4 1.6 - - - -
124D MET* 1.3 78.0 - - - +
126D ASP* 1.3 63.1 + - - +
128D LEU* 3.2 21.2 + - + +
129D TRP* 3.7 4.5 + - - +
182D THR* 3.9 32.8 + - - +
212D VAL* 3.5 24.3 - - + +
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Residues in contact with ASP 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D SER 3.5 5.2 - - - +
125D LYS* 1.3 76.6 + - - +
127D ASP* 1.3 63.6 + - - +
128D LEU 3.2 0.2 - - - -
129D TRP* 3.3 17.9 + - - +
130D SER* 3.2 15.2 + - - -
335D MET 3.7 1.2 - - - +
336D ASP* 3.3 26.4 - - + +
2002D CA 2.4 30.3 - - - -
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Residues in contact with ASP 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D MET* 3.4 19.7 - - + +
124D MET* 3.1 33.6 - - - +
125D LYS 3.1 0.2 - - - -
126D ASP* 1.3 77.4 - - - +
128D LEU* 1.3 62.6 + - - +
130D SER* 3.2 9.9 + - - -
131D ILE* 3.3 17.0 + - - +
333D LEU* 4.7 1.7 - - - +
335D MET 3.1 12.1 - - - +
336D ASP* 3.6 9.5 - - - +
337D SER* 2.6 29.4 + - - +
2002D CA 2.4 27.3 - - - -
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Residues in contact with LEU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D MET* 4.2 11.4 - - - -
120D LEU* 3.7 32.1 - - + -
124D MET 3.4 3.3 + - - +
125D LYS* 3.2 11.9 + - + +
127D ASP* 1.3 77.9 - - - +
129D TRP* 1.3 64.2 + - - +
131D ILE* 3.1 27.5 + - + +
132D GLN* 3.2 8.5 + - - +
153D PHE* 5.2 4.0 - - + -
207D VAL* 4.1 21.4 - - + +
210D GLN* 3.7 14.1 - - + +
211D SER* 3.7 32.3 - - - -
212D VAL* 4.1 8.3 - - + -
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Residues in contact with TRP 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D LYS 3.7 3.4 + - - +
126D ASP* 3.3 16.5 + - + +
128D LEU* 1.3 79.6 - - - +
130D SER* 1.3 61.4 + - - +
131D ILE 3.2 0.2 - - - -
132D GLN* 2.9 63.5 + - - +
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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