Contacts of the strand formed by residues 116 - 129 (chain E) in PDB entry 1SID
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 116 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D CYS* 3.8 16.8 - - + -
20D PRO* 3.1 27.6 + - + +
22D PRO* 5.2 2.5 - - - -
109E ASN* 3.1 9.0 - - - +
111E ASP 3.3 12.5 - - - +
112E LEU* 2.6 53.5 - - + +
114E CYS 2.6 6.9 + - - -
115E ASP* 1.3 77.6 - - - +
117E LEU* 1.3 59.0 + - - +
314E TRP* 3.2 21.4 - - - -
315E VAL 3.4 7.5 + - - -
316E LYS* 4.8 0.2 - - - +
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Residues in contact with LEU 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E ASN* 2.7 24.0 - - + +
110E GLU 4.7 1.8 - - - +
111E ASP* 4.1 10.3 - - - +
115E ASP* 2.7 17.9 + - - +
116E THR* 1.3 76.4 - - - +
118E GLN* 1.3 80.7 + - - +
119E MET* 4.9 13.5 - - + -
314E TRP* 2.8 7.6 - - - -
315E VAL* 2.5 50.5 + - + +
316E LYS 4.7 0.2 - - - -
317E ASN* 4.5 15.0 - - + +
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Residues in contact with GLN 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E GLY 5.3 0.3 - - - +
43E PRO* 4.2 8.1 - - - +
108E LEU* 3.2 30.7 + - + +
109E ASN* 2.4 37.2 + - - +
117E LEU* 1.3 79.4 - - - +
119E MET* 1.3 66.0 + - - +
276E GLU* 5.5 0.2 - - - +
312E LYS* 4.0 36.3 - - + +
313E ARG 3.1 9.9 - - - +
314E TRP* 3.1 41.3 + - + -
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Residues in contact with MET 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E LEU* 4.2 8.7 - - + -
117E LEU* 4.9 13.9 - - + -
118E GLN* 1.3 76.2 - - - +
120E TRP* 1.3 66.7 + - - +
121E GLU 3.5 0.2 + - - -
272E LEU* 4.1 26.2 - - + -
273E CYS 3.6 22.9 - - - +
274E LYS* 5.0 4.5 - - - -
276E GLU* 5.4 6.5 - - - +
311E ARG 3.5 0.9 - - - +
312E LYS* 3.8 3.2 - - - -
313E ARG* 2.9 34.8 + - + +
315E VAL* 3.7 36.6 - - + -
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Residues in contact with TRP 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E LEU* 5.3 6.1 - - + -
41E THR* 4.6 11.0 - - + -
45E SER 5.4 1.1 - - - -
47E THR* 3.9 24.0 - - + -
105E LEU* 3.2 41.1 - - + +
106E PRO* 2.9 44.5 + - + +
108E LEU* 3.6 19.6 - - + +
119E MET* 1.3 77.5 - - - +
121E GLU* 1.3 59.2 + - - +
272E LEU* 3.1 5.0 - - - +
273E CYS* 2.7 46.0 + - + +
276E GLU* 4.7 9.2 - - + -
310E LEU* 3.6 18.2 - - + -
311E ARG* 3.5 22.0 - - - -
312E LYS* 3.8 36.8 - - + -
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Residues in contact with GLU 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E TRP* 1.3 75.4 - - - +
122E ALA* 1.3 90.8 + - - +
123E VAL* 4.2 0.2 - - - -
264E LEU* 3.5 2.3 - - - +
269E VAL 2.6 23.6 - - - +
270E GLY* 3.2 6.2 - - - -
271E PRO 2.8 14.7 - - - +
272E LEU* 3.8 6.7 - - + -
310E LEU* 2.9 5.0 - - - +
311E ARG* 2.6 89.5 + - + +
313E ARG* 3.0 26.2 + - + -
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Residues in contact with ALA 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E TRP 4.2 0.4 - - - -
121E GLU* 1.3 81.2 - - - +
123E VAL* 1.3 58.4 + - - +
167E VAL* 4.7 7.4 - - + -
263E LEU* 3.5 16.7 - - + +
270E GLY* 3.8 0.2 - - - -
271E PRO* 2.6 50.4 + - + +
273E CYS* 5.3 4.7 - - - -
278E LEU* 5.1 5.8 - - + -
308E ILE* 4.0 16.2 - - + -
310E LEU* 3.4 13.3 - - + +
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Residues in contact with VAL 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E GLU* 3.5 16.8 - - - +
122E ALA* 1.3 78.2 - - - +
124E SER* 1.3 63.6 + - - +
262E VAL* 3.3 10.6 - - + +
263E LEU* 2.5 34.5 + - - -
264E LEU* 3.0 28.4 + - + -
309E THR* 2.9 13.2 + - - +
310E LEU* 4.5 2.2 - - - -
311E ARG* 3.8 34.1 - - + +
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Residues in contact with SER 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E VAL* 1.3 82.8 - - - +
125E VAL* 1.3 68.5 + - - +
260E THR* 3.7 16.8 - - - +
261E THR 2.9 13.2 - - - -
262E VAL* 3.9 12.3 - - - -
263E LEU* 3.0 9.5 - - - +
308E ILE* 3.7 0.7 - - - -
309E THR* 3.0 45.1 + - - +
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Residues in contact with VAL 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E SER* 1.3 80.0 - - - +
126E LYS* 1.3 76.9 + - - +
127E THR* 4.0 9.6 + - + +
165E PHE* 5.1 9.6 - - + -
167E VAL* 4.6 13.2 - - + -
240E PHE* 6.2 0.4 - - + -
260E THR* 3.9 1.9 - - - +
261E THR* 2.6 40.4 + - - +
263E LEU* 3.3 32.5 - - + -
306E PHE* 4.6 2.5 - - + -
307E LYS 2.9 13.0 - - - +
308E ILE* 3.8 21.3 - - + -
309E THR* 4.5 0.2 - - - -
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Residues in contact with LYS 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A GLU* 3.0 32.1 + - - +
125E VAL* 1.3 80.8 - - - +
127E THR* 1.3 62.8 + - - +
256E THR 5.8 1.1 - - - +
257E ASN* 3.5 29.0 + - - +
258E THR* 3.5 23.6 + - - +
259E LEU 3.4 21.1 - - - +
260E THR* 3.5 26.2 - - + -
305E TYR* 3.9 5.8 - - + -
307E LYS* 2.7 63.0 + - + +
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Residues in contact with THR 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E VAL* 4.6 9.0 - - + +
126E LYS* 1.3 78.0 - - - +
128E GLU* 1.3 62.8 + - - +
165E PHE* 4.1 22.2 - - + -
256E THR 4.8 5.4 - - - +
259E LEU 4.6 3.1 + - - +
261E THR* 5.6 3.3 + - - +
304E ARG* 2.7 43.3 + - - +
305E TYR* 2.5 23.8 + - - -
306E PHE* 4.0 7.4 - - - -
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Residues in contact with GLU 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A PRO 4.2 3.1 - - - +
231A PRO* 3.8 9.5 - - - +
239A TYR* 2.6 40.5 + - - -
127E THR* 1.3 82.3 + - - +
129E VAL* 1.3 72.2 + - - +
130E VAL* 3.3 18.3 + - + +
254E GLN 4.0 17.0 - - - +
255E PHE* 3.6 13.7 - - - -
256E THR 3.4 23.9 + - - +
257E ASN* 4.7 0.3 - - - -
304E ARG* 3.5 3.3 - - - +
305E TYR* 3.0 38.7 + - + +
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Residues in contact with VAL 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E GLU* 1.3 78.4 - - - +
130E VAL* 1.3 62.3 + - - +
132E SER* 3.5 12.3 + - - -
163E HIS* 4.6 5.2 - - + +
253E LEU* 3.6 38.2 - - + +
254E GLN 5.1 0.6 + - - -
255E PHE* 4.3 3.6 - - - -
284E ASP* 3.3 35.0 - - + +
286E MET* 4.9 0.9 - - - -
302E LEU* 3.5 29.2 - - + -
303E PRO 3.4 7.6 - - - +
304E ARG* 3.4 22.6 - - + +
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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