Contacts of the helix formed by residues 89 - 96 (chain D) in PDB entry 4LQL
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 TRP 89 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D VAL* 4.3 16.2 - - + -
14D GLY* 4.1 17.0 - - - -
15D SER 5.7 1.2 + - - -
54D ALA* 3.7 21.9 - - + +
60D ILE* 3.4 31.2 - - + +
78D THR* 3.9 29.8 - - - -
79D TRP 5.2 1.8 - - - -
80D MET* 4.6 13.9 - - + -
84D SER* 4.3 14.0 - - - -
85D PRO* 3.4 18.5 + - - +
86D ALA* 2.7 17.3 + - - +
88D ASN* 1.3 87.4 - - - +
90D ILE* 1.3 58.5 + - - +
92D GLY* 4.4 2.2 - - - +
93D THR* 3.1 34.9 - - - +
100D LEU* 5.7 5.4 - - + -
133D TYR* 4.5 17.0 - + + -
136D ILE* 4.0 18.7 - - + +
140D LEU* 5.8 0.3 - - - +
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Residues in contact with ILE 90 (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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196C VAL* 4.8 2.2 - - - +
199C GLN* 3.0 71.8 - - + +
200C ILE* 3.7 21.1 - - + -
86D ALA 4.0 1.8 - - - +
87D LYS* 3.6 8.5 - - + +
88D ASN 3.5 2.4 - - - -
89D TRP* 1.3 74.4 - - - +
91D ARG* 1.3 57.8 + - + +
92D GLY 2.7 4.2 + - - +
93D THR* 2.5 26.8 + - - -
94D GLU* 2.6 22.3 + - + -
136D ILE* 3.5 37.5 - - + -
140D LEU* 5.4 4.9 - - + -
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Residues in contact with ARG 91 (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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174C PHE* 3.7 35.6 - - + +
199C GLN* 4.1 13.0 - - - +
203C GLY* 4.5 9.0 - - - +
57D ALA* 5.7 7.2 - - + -
61D THR* 3.3 26.5 - - + +
88D ASN 6.0 1.6 - - - +
90D ILE* 1.3 84.3 - - + +
92D GLY* 1.3 56.6 + - - +
94D GLU* 4.3 8.8 - - - +
95D LEU* 3.1 24.3 + - - +
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Residues in contact with GLY 92 (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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60D ILE* 4.1 9.6 - - - -
61D THR* 3.7 28.7 + - - -
64D MET* 3.7 13.5 - - - +
88D ASN 5.4 1.0 + - - -
89D TRP* 4.4 3.6 - - - -
90D ILE 2.7 4.4 + - - +
91D ARG* 1.3 77.9 - - - +
93D THR* 1.3 55.3 + - - -
95D LEU* 3.0 23.6 - - - +
96D LEU 3.1 9.0 + - - -
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Residues in contact with THR 93 (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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64D MET* 4.8 1.2 - - - +
89D TRP* 3.1 28.0 + - - +
90D ILE* 2.5 12.3 + - - -
92D GLY* 1.3 68.9 - - - +
94D GLU* 1.3 64.7 + - - +
95D LEU 3.1 1.9 + - - -
96D LEU* 3.5 26.5 + - - +
100D LEU* 4.6 16.6 - - - +
136D ILE* 5.1 11.6 + - - +
137D ASN* 5.9 1.6 - - - +
140D LEU* 5.6 6.5 - - - +
142D VAL* 5.1 14.5 - - - +
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Residues in contact with GLU 94 (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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199C GLN 5.2 0.7 - - - +
200C ILE* 3.5 32.3 - - + +
90D ILE* 2.6 29.0 + - + +
91D ARG* 4.3 8.7 - - - +
93D THR* 1.3 72.7 - - - +
95D LEU* 1.3 61.4 + - + +
96D LEU 4.7 1.9 - - - +
140D LEU* 5.7 7.6 - - + +
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Residues in contact with LEU 95 (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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97C GLN* 5.3 16.1 - - + +
61D THR* 4.9 7.9 - - + +
64D MET* 4.9 6.5 - - + -
65D LYS* 5.1 10.1 - - + +
68D ASN* 3.1 12.4 + - - +
91D ARG 3.1 16.2 - - - +
92D GLY* 3.0 19.5 - - - +
93D THR 3.1 0.8 - - - -
94D GLU* 1.3 80.2 - - + +
96D LEU* 1.3 64.0 + - - +
97D GLN* 3.1 8.0 + - - +
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Residues in contact with LEU 96 (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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64D MET* 4.5 15.7 - - + -
67D ALA* 4.8 3.8 - - + -
68D ASN* 3.8 14.1 - - - +
76D VAL* 4.2 14.8 - - + -
92D GLY 3.1 11.9 + - - +
93D THR* 3.5 26.0 + - - +
94D GLU 4.7 2.1 - - - +
95D LEU* 1.3 74.3 - - - +
97D GLN* 1.3 59.7 + - - +
98D LYS* 3.1 39.4 + - + +
99D PRO 3.8 11.0 - - - +
100D LEU* 4.1 25.8 - - + -
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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