Contacts of the helix formed by residues 103 - 121 (chain D) in PDB entry 5LN3
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 THR 103 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D VAL* 1.3 87.2 - - + +
104D VAL* 1.4 64.0 + - - +
105D GLU* 4.0 21.7 + - + +
106D TYR* 3.4 36.2 - - + +
107D ILE* 3.6 5.3 - - - +
137D ASP* 3.4 19.5 + - - -
143D ARG* 5.2 4.0 + - - +
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Residues in contact with VAL 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D VAL* 4.3 16.2 - - + -
103D THR* 1.4 71.6 + - - +
105D GLU* 1.4 66.0 + - + +
106D TYR 3.2 0.2 - - - -
107D ILE* 3.0 25.5 + - + +
108D THR* 3.1 14.0 + - - +
133D ILE* 3.5 29.3 - - + +
134D VAL 4.8 5.6 - - - -
135D GLY 4.4 4.0 - - - -
136D PHE 4.1 9.9 - - - +
137D ASP* 3.7 19.5 - - - +
143D ARG* 3.9 32.8 - - + -
145D TYR* 4.6 9.2 - - + -
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Residues in contact with GLU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D THR* 3.4 19.3 + - + +
104D VAL* 1.4 76.0 - - + +
106D TYR* 1.4 62.7 + - - +
108D THR* 3.1 12.0 + - - -
109D ARG* 3.1 22.5 + - - +
143D ARG* 5.9 1.3 - - + -
145D TYR* 2.8 47.7 + - + -
153D TYR* 3.8 23.6 - - + +
63E SER* 4.4 5.5 + - - -
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Residues in contact with TYR 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1255 TYR* 5.5 2.7 - + - -
1285 ARG* 4.3 14.3 + - - -
1295 ASN* 3.6 27.2 + - - -
1315 GLU* 5.7 2.2 - - - -
94D HIS* 3.5 36.4 + + - -
98D VAL* 5.8 2.0 - - + -
102D VAL* 3.9 29.8 - - + -
103D THR* 3.4 25.0 + - + +
105D GLU* 1.4 80.7 - - - +
107D ILE* 1.3 62.0 + - - +
108D THR 3.3 0.2 + - - -
109D ARG* 3.3 56.6 + - - +
110D TYR* 3.6 6.2 + - - +
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Residues in contact with ILE 107 (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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65D LEU* 4.9 10.3 - - + -
66D ASP* 5.7 5.2 - - + -
69D VAL* 4.3 27.1 - - + -
87D ALA* 4.5 24.2 - - + +
90D GLU* 5.8 8.3 - - + -
91D CYS* 5.8 9.6 - - + -
94D HIS* 6.0 3.4 - - + -
102D VAL* 4.6 14.8 - - + +
103D THR 3.6 15.9 - - - +
104D VAL* 3.0 18.3 + - + +
106D TYR* 1.3 77.0 - - - +
108D THR* 1.4 62.8 + - - +
110D TYR* 3.3 20.7 + - - +
111D ILE* 3.5 12.0 + - + +
133D ILE* 6.0 4.9 - - + -
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Residues in contact with THR 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D VAL* 3.1 15.4 + - - +
105D GLU* 3.1 10.0 + - - -
107D ILE* 1.4 61.8 - - - +
109D ARG* 1.3 64.0 - - - +
111D ILE* 3.2 10.2 - - + +
112D ALA* 3.1 21.7 + - - +
133D ILE* 3.9 24.8 - - + +
145D TYR* 4.5 6.4 - - + +
146D GLN 4.9 0.9 - - - +
147D THR* 2.9 31.0 - - + +
153D TYR* 4.1 24.2 - - + -
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Residues in contact with ARG 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1285 ARG* 4.0 33.6 + - - +
1295 ASN* 3.5 30.9 + - - +
105D GLU* 3.1 11.3 + - - +
106D TYR* 3.4 43.7 - - - +
108D THR* 1.3 78.0 - - - +
110D TYR* 1.3 58.9 + - - +
112D ALA* 3.4 4.4 + - - +
113D SER* 2.9 33.8 + - - +
153D TYR* 3.9 35.0 + - + +
86E LYS* 5.8 7.0 - - - +
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Residues in contact with TYR 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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86D ARG* 3.5 41.1 + - + -
87D ALA* 6.3 0.4 - - - -
90D GLU* 3.5 37.8 + - + -
94D HIS* 6.1 0.2 - - - -
106D TYR 3.6 5.3 + - - +
107D ILE 3.3 13.1 + - - +
108D THR 3.2 0.4 - - - -
109D ARG* 1.3 76.6 - - - +
111D ILE* 1.3 70.5 + - + +
113D SER* 3.1 21.9 + - - -
114D LEU* 3.4 33.6 + - + +
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Residues in contact with ILE 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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71D MET* 4.8 5.4 - - - -
83D VAL* 4.0 34.8 - - + +
86D ARG* 5.4 1.3 - - + -
87D ALA* 5.3 11.4 - - + +
107D ILE* 3.5 10.1 + - + +
108D THR* 3.2 23.3 - - + +
110D TYR* 1.3 84.5 - - + +
112D ALA* 1.3 63.5 - - - +
113D SER 3.4 0.3 + - - -
114D LEU* 3.5 16.3 + - + +
115D LYS* 3.3 35.5 + - - +
131D ALA* 5.3 3.1 - - + -
133D ILE* 4.6 15.5 - - + -
147D THR* 4.1 26.9 - - + +
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Residues in contact with ALA 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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108D THR 3.1 17.5 + - - +
109D ARG* 3.7 8.1 - - - +
111D ILE* 1.3 79.7 - - - +
113D SER* 1.4 62.2 + - - +
115D LYS* 3.1 19.2 + - - +
116D GLN* 3.3 19.8 + - - +
147D THR* 4.5 15.7 - - + -
148D ASP 5.9 0.2 - - - -
151D GLY* 4.4 17.5 - - - -
152D THR 4.8 1.1 - - - +
153D TYR* 4.7 12.3 - - + -
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Residues in contact with SER 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D ARG* 2.9 26.4 + - - +
110D TYR* 3.1 16.9 + - - -
112D ALA* 1.4 75.5 - - - +
114D LEU* 1.3 61.5 + - - +
116D GLN* 3.2 14.8 + - - +
117D ARG* 3.0 33.0 + - - +
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Residues in contact with LEU 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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83D VAL* 6.1 3.1 - - + -
86D ARG* 4.5 22.0 - - + +
110D TYR* 3.5 43.5 - - + +
111D ILE* 3.7 17.9 - - + +
113D SER* 1.3 75.5 - - - +
115D LYS* 1.4 58.4 + - + +
117D ARG* 3.3 8.6 - - - +
118D TYR* 2.9 60.1 + - + +
127D PHE* 5.5 9.0 - - + -
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Residues in contact with LYS 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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83D VAL* 5.0 6.3 - - - +
111D ILE* 3.3 39.2 + - - +
112D ALA* 3.1 10.4 + - - +
114D LEU* 1.4 75.7 - - + +
116D GLN* 1.4 61.6 + - - +
118D TYR* 3.2 12.3 + - - -
119D THR* 3.3 14.7 + - - -
126D PRO* 3.6 27.1 - - + +
127D PHE* 4.1 20.0 - - + -
129D ILE* 3.9 37.3 + - - +
147D THR* 4.4 11.3 - - - +
148D ASP 4.5 2.4 + - - +
149D PRO* 4.1 26.5 - - + -
151D GLY* 4.8 8.5 - - - -
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Residues in contact with GLN 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 ALA* 3.3 13.3 + - - +
113D SER* 3.2 19.2 + - - +
115D LYS* 1.4 74.8 - - - +
117D ARG* 1.4 64.5 + - + +
119D THR* 3.3 10.0 + - - -
120D GLN* 3.0 31.9 + - - +
150D SER 5.4 0.2 - - - +
151D GLY* 3.1 31.8 + - - -
83E ALA* 2.9 42.6 + - + +
84E ASP* 5.3 3.1 - - - +
86E LYS* 4.0 9.9 - - - +
87E THR* 2.9 23.6 + - - +
135E ARG* 4.6 1.2 + - - -
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Residues in contact with ARG 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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113D SER* 3.0 29.9 + - - +
114D LEU* 3.3 9.9 - - - +
116D GLN* 1.4 79.0 - - + +
118D TYR* 1.3 60.6 + - + +
120D GLN* 3.3 6.3 + - - +
121D SER* 2.8 40.4 + - - -
87E THR* 4.9 19.5 - - - +
91E LYS* 4.7 14.8 - - - +
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Residues in contact with TYR 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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114D LEU* 2.9 51.6 + - + +
115D LYS* 3.2 7.1 + - - +
117D ARG* 1.3 79.3 - - + +
119D THR* 1.4 56.0 + - - +
121D SER* 3.2 17.0 - - - +
124D ARG* 3.2 66.0 + - + +
125D ARG* 3.5 33.7 - - - +
126D PRO* 3.7 10.1 - - + -
127D PHE* 4.0 20.9 - + - -
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Residues in contact with THR 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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8D THR* 4.3 13.6 + - - +
16D LEU* 5.0 12.1 - - + -
18D GLN* 5.4 4.7 - - - +
19D VAL* 4.6 20.3 - - + +
115D LYS 3.3 12.5 + - - -
116D GLN* 3.3 11.0 + - - -
118D TYR* 1.4 73.9 - - - +
120D GLN* 1.3 63.1 + - - +
121D SER 3.6 5.0 - - - +
124D ARG 5.2 0.9 - - - -
125D ARG* 5.2 0.4 - - - +
126D PRO* 3.7 18.0 - - + +
134E SER* 4.1 3.6 + - - -
135E ARG* 3.2 32.9 + - - +
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Residues in contact with GLN 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 GLN 3.0 17.9 + - - +
117D ARG* 4.0 6.3 - - - +
119D THR* 1.3 76.8 - - - +
121D SER* 1.4 60.3 + - - +
84E ASP* 3.1 29.7 + - - +
87E THR* 5.5 12.6 - - + +
133E MET* 3.3 38.0 - - + +
134E SER* 3.4 5.9 + - - -
135E ARG* 2.9 44.7 - - - +
136E PRO 3.5 20.8 + - - -
137E PHE* 3.9 12.1 - - + -
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Residues in contact with SER 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D THR* 4.2 5.5 - - - +
117D ARG* 2.8 27.3 + - - -
118D TYR* 3.2 25.1 + - - +
119D THR 3.6 4.9 - - - +
120D GLN* 1.4 79.2 - - - +
122D ASN* 1.3 68.5 + - - +
123D GLY 4.0 0.3 + - - -
124D ARG* 4.0 10.2 - - - +
132E ALA 3.3 15.7 - - - -
133E MET* 4.1 0.7 - - - +
134E SER* 4.3 1.6 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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