Contacts of the helix formed by residues 122 - 129 (chain J) in PDB entry 6ALG
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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A A 4.6 7.6 + - - -
116J PHE 3.4 8.2 + - - -
117J LEU* 3.3 27.0 + - - +
119J SER* 4.0 3.8 - - - -
120J LEU* 3.9 4.1 - - - +
121J PRO* 1.3 70.4 - - - +
123J ARG* 1.3 59.3 + - - +
124J ILE* 4.0 2.1 - - - +
125J GLY* 2.8 30.4 + - - -
126J LEU* 2.9 34.4 + - - +
132J LEU* 3.7 19.2 - - - +
135J ILE* 5.2 1.0 - - - +
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Residues in contact with ARG 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116J PHE* 3.5 19.0 + - + +
119J SER* 4.5 6.0 + - - +
121J PRO* 3.4 31.4 + - - +
122J SER* 1.3 70.0 + - - +
124J ILE* 1.3 60.8 + - - +
126J LEU* 4.8 10.7 - - - +
127J LEU* 2.8 33.1 + - - +
223J LEU* 3.8 32.7 - - + +
237J MET* 4.1 23.1 - - + -
1330J ARG* 5.4 2.2 + - - +
1333J THR* 4.9 8.5 + - - +
1334J GLU* 3.7 35.7 + - - +
1337J VAL* 3.9 29.3 - - + +
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Residues in contact with ILE 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J ALA* 5.2 3.6 - - + -
113J HIS 4.9 3.4 - - - +
116J PHE* 3.3 31.0 + - + +
117J LEU* 4.3 14.1 - - + +
122J SER* 4.1 1.6 - - - +
123J ARG* 1.3 75.5 - - - +
125J GLY* 1.3 56.6 + - - +
127J LEU* 3.7 5.6 - - - +
128J LEU* 3.0 50.7 + - + +
135J ILE* 4.4 13.5 - - + -
139J LEU* 6.2 0.2 - - + -
185J ILE* 3.9 15.9 - - + -
189J LEU* 4.7 6.7 - - + -
237J MET* 3.8 31.0 - - + +
238J ILE* 4.6 16.4 - - + -
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Residues in contact with GLY 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122J SER* 2.8 25.5 + - - -
123J ARG 3.2 0.4 - - - -
124J ILE* 1.3 78.4 - - - +
126J LEU* 1.3 56.6 + - - +
127J LEU 3.1 0.2 - - - -
128J LEU* 3.2 0.5 + - - +
129J ASP 3.1 21.0 + - - -
130J MET 3.3 17.1 + - - +
132J LEU* 5.6 2.2 - - - -
135J ILE* 3.8 17.5 - - - +
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Residues in contact with LEU 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A A 5.8 2.2 - - - +
121J PRO* 3.9 24.7 - - + -
122J SER* 2.9 25.9 + - - +
123J ARG* 4.8 9.9 - - - +
125J GLY* 1.3 71.4 - - - -
127J LEU* 1.3 60.1 + - - +
128J LEU 3.4 0.2 - - - -
129J ASP* 4.1 4.7 - - - +
216J LYS 6.2 0.2 - - - +
219J LYS* 4.1 38.6 - - + +
220J ARG* 3.3 31.9 + - + +
223J LEU* 3.7 34.5 - - + +
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Residues in contact with LEU 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J ARG 2.8 21.8 + - - +
124J ILE* 3.7 5.4 - - - +
125J GLY 3.1 0.2 - - - -
126J LEU* 1.3 80.0 - - - +
128J LEU* 1.3 57.7 + - - +
129J ASP 3.5 0.2 - - - -
189J LEU* 3.8 27.4 - - + -
192J MET* 3.7 15.6 - - - +
194J LEU* 4.9 3.6 - - + -
220J ARG* 2.9 21.3 + - + +
223J LEU* 4.0 15.3 - - + -
224J LEU* 3.7 30.1 - - + -
227J PHE* 5.2 6.3 - - + -
234J PRO* 3.8 18.6 - - + -
237J MET* 4.4 20.6 - - + -
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Residues in contact with LEU 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J ILE* 3.0 36.3 + - + +
125J GLY 4.1 0.7 - - - +
127J LEU* 1.3 76.8 - - - +
129J ASP* 1.3 68.1 + - - +
130J MET* 4.0 15.0 - - + -
135J ILE* 4.5 7.9 - - + -
157J GLN* 3.2 28.3 + - - +
185J ILE* 4.0 26.5 - - + -
188J LEU* 4.1 26.7 - - + -
189J LEU* 3.7 26.7 - - + -
192J MET* 3.8 17.0 - - + -
220J ARG* 4.0 3.5 + - - +
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Residues in contact with ASP 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J GLY 3.1 6.0 + - - -
126J LEU* 4.1 4.2 - - - +
127J LEU 3.5 3.2 - - - -
128J LEU* 1.3 80.6 - - - +
130J MET* 1.3 57.1 + - - +
131J PRO* 4.8 0.3 - - - +
157J GLN* 4.5 7.1 - - + +
216J LYS* 4.1 17.7 + - - -
217J LEU* 6.0 2.3 - - - +
220J ARG* 3.8 30.2 + - - +
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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