Contacts of the helix formed by residues 122 - 129 (chain D) in PDB entry 6K4Y
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 SER 122 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D PHE 3.5 7.6 + - - -
117D LEU* 3.4 28.3 + - - +
119D SER* 3.9 4.0 - - - -
120D LEU* 3.9 4.3 - - - +
121D PRO* 1.3 69.6 - - - +
123D ARG* 1.3 59.9 + - - +
124D ILE* 4.1 1.6 - - - +
125D GLY* 2.8 25.3 + - - -
126D LEU* 3.0 32.9 + - - +
132D LEU* 3.8 18.6 - - - +
135D ILE* 5.3 1.2 - - - +
56N T 5.8 1.2 + - - -
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Residues in contact with ARG 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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115D TRP 5.1 0.7 - - - +
116D PHE* 3.5 33.3 + - + +
119D SER* 4.3 7.9 + - - +
121D PRO* 4.0 32.9 + - - +
122D SER* 1.3 70.9 + - - +
124D ILE* 1.3 55.4 + - - +
126D LEU* 4.8 9.6 - - - +
127D LEU* 2.7 41.5 + - + +
219D LYS* 6.2 1.2 - - - +
223D LEU* 4.0 30.7 - - + +
237D MET* 4.7 7.6 - - + -
1330D ARG* 5.2 4.2 + - - +
1333D THR* 4.9 9.7 + - - -
1334D GLU* 3.4 39.9 - - - +
1337D VAL* 4.5 21.0 - - + +
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Residues in contact with ILE 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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112D ALA* 5.2 1.6 - - + -
113D HIS 5.0 3.4 - - - +
116D PHE* 3.3 32.6 + - + +
117D LEU* 4.4 17.0 - - + +
122D SER* 4.2 1.8 - - - +
123D ARG* 1.3 75.2 - - - +
125D GLY* 1.3 57.7 + - - +
127D LEU* 4.2 6.1 - - - -
128D LEU* 2.9 46.5 + - + +
135D ILE* 4.5 16.6 - - + -
185D ILE* 4.5 14.4 - - + -
189D LEU* 4.4 10.8 - - + -
237D MET* 4.2 22.4 - - + +
238D ILE* 4.7 18.8 - - + -
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Residues in contact with GLY 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 SER* 2.8 24.7 + - - -
123D ARG 3.2 0.2 - - - -
124D ILE* 1.3 77.6 - - - +
126D LEU* 1.3 58.3 + - - +
128D LEU* 3.3 0.7 + - - +
129D ASP 3.1 20.3 + - - -
130D MET* 3.1 20.7 + - - +
132D LEU* 5.9 1.8 - - - -
135D ILE* 3.7 18.6 - - - +
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Residues in contact with LEU 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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121D PRO* 3.7 27.6 - - + -
122D SER 3.0 26.0 + - - +
123D ARG* 4.5 9.0 - - - +
125D GLY* 1.3 71.2 - - - -
127D LEU* 1.3 64.3 + - - +
128D LEU 3.3 0.2 - - - -
129D ASP* 3.5 10.0 + - - +
219D LYS* 4.4 22.4 - - + +
220D ARG* 3.2 40.4 + - + +
223D LEU* 3.7 31.9 - - + -
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Residues in contact with LEU 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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123D ARG* 2.7 22.1 + - + +
124D ILE* 3.8 4.3 - - - +
126D LEU* 1.3 78.9 - - - +
128D LEU* 1.3 63.5 + - + +
189D LEU* 4.2 16.4 - - + -
192D MET* 3.4 18.0 - - - +
194D LEU* 5.4 3.1 - - + -
220D ARG* 3.3 22.2 + - - +
223D LEU* 4.2 20.2 - - + +
224D LEU* 3.7 30.1 - - + -
227D PHE* 5.7 12.3 - - + -
234D PRO* 4.8 6.7 - - + -
237D MET* 3.9 28.0 - - + -
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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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124D ILE* 2.9 30.0 + - + +
125D GLY 4.0 2.0 - - - +
127D LEU* 1.3 84.6 - - + +
129D ASP* 1.3 70.1 + - - +
130D MET* 4.1 17.7 - - + -
135D ILE* 5.1 1.8 - - + -
156D ARG* 4.8 0.9 - - - +
157D GLN* 3.4 46.0 + - - +
185D ILE* 6.1 4.3 - - + -
188D LEU* 4.3 19.5 - - + -
189D LEU* 4.0 29.4 - - + +
192D MET* 3.7 21.1 - - + +
220D ARG* 4.8 1.6 - - - -
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Residues in contact with ASP 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 GLY 3.1 5.4 + - - -
126D LEU* 3.5 8.1 + - - +
127D LEU 3.3 3.8 - - - -
128D LEU* 1.3 81.0 - - - +
130D MET* 1.3 59.4 + - - +
131D PRO* 4.8 0.7 - - - +
157D GLN* 4.9 4.2 - - - +
217D LEU* 6.1 1.6 - - - +
220D ARG* 3.4 28.1 + - - +
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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