Contacts of the helix formed by residues 107 - 120 (chain D) in PDB entry 3LL8
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 107 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C ASP* 2.5 32.9 + - - -
105D TYR 3.7 1.9 + - - -
106D ILE* 1.3 79.8 - - - +
108D ASN* 1.3 58.7 + - - +
110D GLU* 3.0 25.0 + - - +
111D LEU* 3.0 26.5 + - - +
136D ILE* 4.5 2.7 - - - -
146D ARG* 4.5 17.7 - - - -
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Residues in contact with ASN 108 (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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14C THR* 5.0 4.5 - - - +
15C ASP* 3.8 5.4 + - - +
16C ARG* 3.5 24.8 - - + +
17C VAL 4.7 0.3 + - - -
23C PHE* 3.9 11.5 - - - -
107D SER* 1.3 73.5 - - - +
109D GLY* 1.3 57.4 + - - +
111D LEU 3.5 0.7 + - - -
112D PHE* 3.1 26.5 + - - +
129D GLN* 2.9 25.4 + - - +
132D VAL* 3.6 9.7 - - - +
133D ASP* 3.0 22.4 + - - +
136D ILE* 3.6 27.8 - - + +
145D GLY 4.5 8.7 + - - +
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Residues in contact with GLY 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ASP* 2.9 41.3 + - - -
16C ARG* 4.6 0.7 - - - -
17C VAL* 4.1 10.7 - - - +
108D ASN* 1.3 75.3 + - - +
110D GLU* 1.3 64.1 + - - +
112D PHE* 3.6 1.6 + - - +
113D GLN* 3.1 35.0 + - - +
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Residues in contact with GLU 110 (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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15C ASP* 3.8 3.8 + - - +
98D TYR 3.5 13.9 - - - +
99D ASP* 3.6 2.1 - - - +
100D MET* 3.6 27.5 - - + +
101D ASP* 2.9 30.4 + - - +
105D TYR 3.1 3.3 - - - +
106D ILE* 3.4 4.4 - - + -
107D SER* 3.0 34.5 + - - +
109D GLY* 1.3 74.7 - - - +
111D LEU* 1.3 60.1 + - - +
113D GLN* 3.2 3.5 + - - +
114D VAL* 2.9 35.5 + - - +
510D CA 2.4 30.7 - - - -
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Residues in contact with LEU 111 (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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349C VAL* 3.8 29.8 - - + -
350C PHE* 3.7 29.4 - - + -
98D TYR* 3.7 28.0 - - + -
106D ILE* 3.9 9.8 - - + +
107D SER 3.0 17.6 + - - +
108D ASN 3.8 3.8 - - - +
109D GLY 3.3 0.2 - - - -
110D GLU* 1.3 76.9 - - - +
112D PHE* 1.3 62.9 + - - +
114D VAL* 4.1 2.3 - - - +
115D LEU* 3.1 37.5 + - + +
132D VAL* 4.1 11.2 - - + +
135D THR* 4.2 4.0 - - + -
136D ILE* 4.1 24.9 - - + -
147D ILE* 5.5 0.2 - - + -
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Residues in contact with PHE 112 (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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17C VAL* 3.6 31.0 - - + -
18C VAL* 3.7 22.7 - - + -
108D ASN* 3.1 18.4 + - - +
109D GLY 3.8 4.5 - - - +
111D LEU* 1.3 76.3 - - - +
113D GLN* 1.3 64.1 + - + +
115D LEU 3.2 1.7 + - - -
116D LYS* 2.8 45.5 + - + +
125D ASP* 3.6 40.8 - - - -
128D LEU* 3.6 27.9 - - + +
129D GLN* 3.8 27.6 - - - +
132D VAL* 3.9 12.4 - - + +
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Residues in contact with GLN 113 (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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15C ASP* 5.4 2.3 - - - +
17C VAL* 4.5 14.3 - - + +
100D MET* 4.0 28.6 - - + +
109D GLY* 3.1 29.2 + - - +
110D GLU* 3.2 6.0 + - - +
112D PHE* 1.3 78.7 - - + +
114D VAL* 1.3 63.8 + - - +
116D LYS* 3.3 8.8 + - - +
117D MET* 3.0 29.0 + - + +
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Residues in contact with VAL 114 (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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53D LEU* 4.7 7.4 - - + -
56D ARG* 4.6 2.2 - - + -
97D ILE* 3.8 28.9 - - + +
98D TYR* 3.9 25.8 - - + +
100D MET* 3.7 28.9 - - + -
110D GLU 2.9 20.4 + - - +
111D LEU 4.2 2.0 - - - +
113D GLN* 1.3 76.4 - - - +
115D LEU* 1.3 61.8 + - - +
117D MET* 3.3 28.8 + - + +
118D MET* 3.4 25.9 + - + +
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Residues in contact with LEU 115 (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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349C VAL* 3.6 34.5 - - + -
352C TRP* 4.5 13.0 - - + -
353C SER* 3.7 33.4 - - - +
98D TYR* 5.0 2.5 - - + -
111D LEU* 3.1 28.3 + - + +
112D PHE 3.7 0.9 - - - +
114D VAL* 1.3 72.7 - - - +
116D LYS* 1.3 60.5 + - - +
118D MET* 2.9 12.2 + - + -
119D VAL* 2.8 37.5 + - + +
128D LEU* 3.5 31.9 - - + -
132D VAL* 3.6 13.0 - - + -
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Residues in contact with LYS 116 (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 PHE* 2.8 30.6 + - + +
113D GLN* 3.4 10.3 - - - +
115D LEU* 1.3 76.4 - - - +
117D MET* 1.3 62.1 + - - +
119D VAL* 4.5 2.0 - - + +
120D GLY* 3.0 50.3 + - - +
121D ASN* 3.9 15.2 + - - +
123D LEU 4.4 9.6 + - - +
125D ASP* 3.9 20.5 + - - +
128D LEU* 3.9 17.0 - - + +
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Residues in contact with MET 117 (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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52D PRO* 3.4 36.4 - - + +
53D LEU* 4.5 4.7 - - + -
55D GLN* 6.5 0.7 - - - -
56D ARG* 3.9 28.0 - - - -
100D MET* 3.7 29.6 - - + -
113D GLN* 3.0 25.2 + - + +
114D VAL* 3.3 18.6 + - + +
116D LYS* 1.3 74.6 - - - +
118D MET* 1.3 64.4 + - + +
120D GLY* 4.6 2.4 + - - -
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Residues in contact with MET 118 (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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353C SER* 4.0 22.0 - - - +
356C PHE* 3.4 47.1 - - + -
357C VAL* 3.6 26.0 - - + -
52D PRO* 4.6 4.1 - - + +
53D LEU* 3.9 18.4 - - + -
98D TYR* 4.4 2.7 - - + -
114D VAL* 3.5 37.9 - - + +
115D LEU* 2.9 14.5 + - + +
117D MET* 1.3 80.0 - - - +
119D VAL* 1.3 65.4 + - + +
120D GLY 3.4 0.4 - - - -
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Residues in contact with VAL 119 (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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352C TRP* 3.6 34.8 - - + -
115D LEU* 2.8 30.3 + - + +
116D LYS* 4.9 2.0 - - - -
118D MET* 1.3 80.1 - - + +
120D GLY* 1.3 68.4 + - - +
121D ASN 3.3 0.3 + - - -
122D ASN* 3.2 30.3 + - + +
123D LEU* 3.7 42.6 - - + +
128D LEU* 5.2 4.3 - - + -
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Residues in contact with GLY 120 (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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116D LYS* 3.0 39.1 + - - +
117D MET 4.5 2.6 - - - -
118D MET 3.4 2.0 - - - -
119D VAL* 1.3 80.4 - - - +
121D ASN* 1.3 63.2 + - - -
122D ASN 3.6 0.7 + - - -
123D LEU 4.3 3.3 - - - +
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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