Contacts of the helix formed by residues 124 - 140 (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 LYS 124 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A THR* 4.9 13.7 - - - +
246A GLU* 3.6 26.6 + - + +
123D LEU* 1.3 76.7 - - - +
125D ASP* 1.3 65.7 + - - +
126D THR* 3.3 8.2 + - - +
127D GLN* 3.0 37.5 + - + +
128D LEU* 3.1 21.0 + - - +
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Residues in contact with ASP 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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17C VAL* 5.4 2.3 - - - +
18C VAL* 3.7 21.1 - - + +
112D PHE* 3.6 22.8 - - - -
116D LYS* 3.9 27.0 + - - +
124D LYS* 1.3 73.8 - - - +
126D THR* 1.3 57.4 + - - +
128D LEU* 4.8 1.1 - - - -
129D GLN* 3.0 30.5 + - - +
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Residues in contact with THR 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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18C VAL* 4.7 4.7 - - - +
21C VAL* 4.1 22.6 - - + +
124D LYS* 3.2 8.1 - - - +
125D ASP* 1.3 75.2 - - - +
127D GLN* 1.3 65.0 + - + +
129D GLN* 3.5 1.9 + - - +
130D GLN* 3.0 51.5 + - - +
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Residues in contact with GLN 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU* 6.0 0.3 - - - +
341C TYR* 3.8 50.7 - - + -
122D ASN 4.6 1.4 - - - +
123D LEU* 3.5 17.2 - - + +
124D LYS* 3.0 53.8 + - + +
126D THR* 1.3 77.8 - - + +
128D LEU* 1.3 64.2 + - - +
130D GLN* 3.2 3.8 + - - +
131D ILE* 3.1 30.2 + - - +
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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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352C TRP* 5.3 0.2 - - + -
112D PHE* 3.6 45.5 - - + +
115D LEU* 3.5 36.1 - - + -
116D LYS* 3.9 26.2 - - + +
119D VAL* 5.2 6.1 - - + -
123D LEU* 4.3 18.3 - - + +
124D LYS 3.1 16.0 + - - +
125D ASP* 4.8 0.4 - - - -
127D GLN* 1.3 76.0 - - - +
129D GLN* 1.3 57.7 + - - +
131D ILE* 3.3 19.4 - - + +
132D VAL* 3.0 35.4 + - + +
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Residues in contact with GLN 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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16C ARG* 3.4 21.3 - - - +
17C VAL 3.5 10.0 + - - -
18C VAL* 3.0 47.2 + - + +
21C VAL* 3.9 8.3 - - + -
108D ASN* 2.9 19.3 + - - +
112D PHE* 3.8 14.7 - - + -
125D ASP 3.0 18.4 + - - +
126D THR 3.7 4.0 - - - +
128D LEU* 1.3 78.6 - - - +
130D GLN* 1.3 56.8 + - - +
132D VAL* 4.1 5.2 - - - +
133D ASP* 2.9 60.4 + - - -
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Residues in contact with GLN 130 (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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21C VAL* 3.7 21.0 - - + +
22C PRO* 5.2 7.6 + - - +
24C PRO* 5.8 0.2 - - - +
53C GLU* 5.4 2.4 + - - +
339C HIS 4.7 0.9 + - - +
340C PRO* 3.5 19.8 - - + +
341C TYR* 2.9 33.4 + - - +
126D THR* 3.0 38.1 + - - +
127D GLN* 3.2 4.4 + - - +
129D GLN* 1.3 75.2 - - - +
131D ILE* 1.3 59.5 + - - +
133D ASP* 3.4 8.2 + - - +
134D LYS* 3.1 43.9 + - - +
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Residues in contact with ILE 131 (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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341C TYR* 3.6 41.5 - - + +
342C TRP* 4.2 1.8 - - + -
343C LEU* 3.6 40.4 - - + +
347C MET 5.9 0.9 - - - +
349C VAL* 3.7 23.3 - - + -
352C TRP* 4.5 2.0 - - + -
123D LEU* 3.7 24.0 - - + -
127D GLN 3.1 5.8 + - - +
128D LEU* 3.3 18.2 - - + +
130D GLN* 1.3 73.9 - - - +
132D VAL* 1.3 58.9 + - - +
134D LYS* 3.9 7.4 - - - +
135D THR* 2.8 34.2 + - - -
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Residues in contact with VAL 132 (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* 4.7 1.3 - - - -
108D ASN* 3.6 39.5 - - - +
111D LEU* 4.1 9.4 - - + +
112D PHE* 3.9 19.1 - - + +
115D LEU* 3.6 29.4 - - + -
128D LEU* 3.0 24.7 + - + +
129D GLN* 3.7 7.0 - - - +
130D GLN 3.3 0.2 - - - -
131D ILE* 1.3 74.1 - - - +
133D ASP* 1.3 65.1 + - - +
135D THR* 3.1 7.6 + - - -
136D ILE* 3.0 30.4 + - + +
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Residues in contact with ASP 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ARG* 2.7 28.5 + - - -
21C VAL* 4.3 1.7 - - - +
22C PRO 4.2 7.3 - - - +
23C PHE* 3.3 23.4 - - + -
24C PRO* 4.3 12.5 - - + +
108D ASN* 3.0 17.2 + - - +
129D GLN* 2.9 41.0 + - - +
130D GLN* 3.6 7.3 - - - +
132D VAL* 1.3 75.9 - - - +
134D LYS* 1.3 57.1 + - - +
136D ILE* 3.2 3.6 + - - +
137D ILE* 3.0 33.3 + - - +
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Residues in contact with LYS 134 (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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24C PRO* 4.5 17.0 - - + -
53C GLU* 2.8 37.3 + - + +
340C PRO* 4.1 5.5 - - - +
341C TYR 2.8 29.5 + - - -
342C TRP* 3.6 44.1 - - + +
130D GLN* 3.1 24.7 + - - +
131D ILE* 4.1 7.0 - - - +
133D ASP* 1.3 79.8 - - - +
135D THR* 1.3 62.8 + - - +
137D ILE* 4.0 7.8 - - + +
138D ASN* 3.1 24.3 + - - +
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Residues in contact with THR 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C ASP* 3.6 16.4 - - + +
349C VAL* 2.9 45.9 + - + +
350C PHE* 3.7 30.1 - - + -
111D LEU* 4.2 4.3 - - + -
131D ILE 2.8 21.6 + - - -
132D VAL 3.1 4.7 + - - -
134D LYS* 1.3 78.7 - - - +
136D ILE* 1.3 58.5 + - - +
138D ASN* 3.5 4.1 + - - +
139D ALA* 3.0 28.2 + - + +
155D VAL* 6.0 0.4 - - + -
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Residues in contact with ILE 136 (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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23C PHE* 5.4 7.9 - - + -
106D ILE 5.2 0.2 - - - +
107D SER 4.5 2.5 - - - -
108D ASN* 3.6 50.3 - - + +
111D LEU* 4.1 15.7 - - + -
132D VAL* 3.0 20.3 + - + +
133D ASP* 3.8 4.5 - - - +
135D THR* 1.3 75.9 - - - +
137D ILE* 1.3 57.5 + - + +
140D ASP* 2.8 48.3 + - + +
145D GLY* 3.7 23.6 - - - +
147D ILE* 3.9 26.2 - - + -
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Residues in contact with ILE 137 (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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23C PHE* 3.6 22.4 - - + -
24C PRO* 3.4 49.6 - - + +
25C PRO 5.0 2.0 - - - +
26C SER* 3.6 27.8 - - - +
55C ARG* 4.9 16.6 + - - +
133D ASP 3.0 21.3 + - - +
134D LYS* 4.0 7.9 - - + +
136D ILE* 1.3 75.2 - - - +
138D ASN* 1.3 62.1 + - - +
140D ASP* 4.0 10.1 + - - +
141D LYS* 5.5 1.7 - - - +
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Residues in contact with ASN 138 (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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55C ARG* 5.5 11.7 - - - +
168C ILE* 5.1 12.3 + - - +
348C ASP* 5.1 9.6 - - + +
134D LYS 3.1 17.6 + - - +
135D THR* 3.7 6.1 - - - +
137D ILE* 1.3 78.0 - - - +
139D ALA* 1.3 60.1 + - - +
141D LYS* 2.8 33.2 + - - +
155D VAL* 4.7 14.9 - - - +
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Residues in contact with ALA 139 (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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350C PHE* 4.9 4.9 - - + -
135D THR* 3.0 16.9 + - + +
138D ASN* 1.3 77.6 - - - +
140D ASP* 1.3 60.5 + - - +
141D LYS* 2.9 17.5 + - - +
147D ILE* 3.8 20.6 - - + -
151D GLU* 3.5 22.0 - - - +
155D VAL* 3.5 32.1 - - + -
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Residues in contact with ASP 140 (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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136D ILE* 2.8 33.5 + - + +
137D ILE* 4.0 7.0 + - - +
138D ASN 3.6 1.2 - - - -
139D ALA* 1.3 69.6 - - - +
141D LYS* 1.3 57.0 + - - +
142D ASP* 2.9 10.0 + - - +
143D GLY* 3.2 13.5 + - - -
144D ASP* 2.8 12.6 + - - +
145D GLY* 2.7 30.2 + - - -
146D ARG 3.6 5.6 - - - -
147D ILE* 3.8 6.3 - - + +
151D GLU* 3.9 2.2 - - - -
511D CA 2.2 32.6 - - - -
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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