Contacts of the strand formed by residues 117 - 130 (chain C) 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 LEU 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109C ASN* 3.3 39.3 - - + +
111C ASP* 3.6 26.7 - - + +
112C LEU* 5.4 5.4 - - + -
115C ASP 2.8 9.4 + - - +
116C THR* 1.3 79.0 - - - +
118C GLN* 1.3 90.6 + - - +
119C MET* 5.2 3.8 - - + -
276C GLU* 5.8 3.8 - - - +
314C TRP* 3.2 5.4 - - - -
315C VAL* 2.7 46.0 + - + +
317C ASN* 4.4 17.2 - - - +
318C PRO* 4.9 3.8 - - + -
319C TYR* 6.5 2.9 - - + -
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Residues in contact with GLN 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C GLY 4.3 4.8 + - - -
43C PRO* 4.7 8.7 - - - +
108C LEU* 3.7 39.4 + - + +
109C ASN* 3.7 19.3 + - - +
117C LEU* 1.3 95.1 - - - +
119C MET* 1.3 61.9 + - - +
276C GLU* 5.7 0.7 - - - +
312C LYS* 4.0 27.3 - - - +
313C ARG 3.0 10.1 - - - +
314C TRP* 3.1 48.0 + - + -
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Residues in contact with MET 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C LEU* 4.3 11.2 - - - -
117C LEU* 5.2 3.1 - - + -
118C GLN* 1.3 76.7 - - - +
120C TRP* 1.3 68.4 + - - +
121C GLU* 4.0 1.4 - - - +
272C LEU* 4.2 19.3 - - + -
273C CYS 4.0 17.5 - - - +
274C LYS* 4.7 9.4 - - + -
275C GLY 5.5 0.7 - - - +
276C GLU* 4.3 15.5 - - - +
312C LYS 3.7 0.2 - - - -
313C ARG* 2.7 45.0 + - - +
315C VAL* 3.5 23.3 - - + -
318C PRO* 4.9 7.0 - - + -
362F GLY* 3.4 40.8 - - - +
363F ASP 4.5 0.7 - - - +
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Residues in contact with TRP 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 4.8 7.2 - - + -
41C THR* 4.7 7.2 - - + -
45C SER 4.5 2.5 - - - -
47C THR* 3.7 24.0 - - - -
105C LEU* 3.0 42.4 - - + +
106C PRO* 2.9 39.8 + - + +
108C LEU* 3.0 23.4 - - + +
119C MET* 1.3 76.1 - - - +
121C GLU* 1.3 61.5 + - - +
272C LEU* 3.2 5.7 - - - +
273C CYS* 2.8 47.4 + - + +
276C GLU* 4.3 10.7 + - - +
310C LEU* 4.3 13.5 - - + -
311C ARG 3.4 16.2 - - - -
312C LYS* 3.5 37.2 - - + -
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Residues in contact with GLU 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C MET 4.0 5.6 - - - +
120C TRP* 1.3 78.5 - - - +
122C ALA* 1.3 75.1 + - - +
123C VAL* 3.5 7.3 + - - +
269C VAL 2.8 22.7 - - - +
271C PRO 2.9 20.4 - - - +
272C LEU* 3.9 13.7 - - + -
273C CYS* 4.6 0.2 - - - -
310C LEU* 3.1 3.3 - - - +
311C ARG* 2.7 82.7 + - + +
313C ARG* 3.0 25.8 + - + +
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Residues in contact with ALA 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C GLU* 1.3 83.0 - - - +
123C VAL* 1.3 60.8 + - - +
167C VAL* 4.7 6.3 - - + -
263C LEU* 4.3 6.7 - - + -
270C GLY* 3.5 2.6 - - - -
271C PRO* 2.7 47.9 + - + +
273C CYS* 4.6 4.8 - - - -
278C LEU* 5.1 6.5 - - + -
308C ILE* 3.8 22.9 - - + -
309C THR 3.6 4.3 - - - -
310C LEU* 4.1 9.1 - - + +
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Residues in contact with VAL 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C GLU* 3.5 20.6 - - - +
122C ALA* 1.3 80.3 - - - +
124C SER* 1.3 65.6 + - - +
262C VAL* 3.2 9.6 - - + +
263C LEU* 2.5 37.0 + - - +
264C LEU* 3.2 26.2 + - + -
309C THR* 2.7 19.9 + - - +
310C LEU 4.8 0.2 - - - -
311C ARG* 4.0 24.7 - - + +
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Residues in contact with SER 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C VAL* 1.3 89.1 - - - +
125C VAL* 1.3 67.5 + - - +
260C THR* 4.0 15.5 - - - +
261C THR 2.9 19.1 - - - -
262C VAL* 4.1 6.5 - - - -
263C LEU* 3.4 5.1 - - - +
308C ILE* 3.5 1.2 - - - +
309C THR* 2.9 45.4 + - - +
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Residues in contact with VAL 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C SER* 1.3 79.4 - - - +
126C LYS* 1.3 75.3 + - - +
127C THR* 4.1 2.4 + - + +
165C PHE* 4.8 9.2 - - + -
167C VAL* 4.1 15.0 - - + -
260C THR* 4.1 1.5 - - - +
261C THR* 2.8 41.5 + - - +
263C LEU* 3.6 28.0 - - + -
306C PHE* 4.4 9.9 - - + -
307C LYS 2.9 17.5 - - - +
308C ILE* 3.6 21.3 - - + -
309C THR* 4.4 0.4 - - - -
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Residues in contact with LYS 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C VAL* 1.3 76.4 - - - +
127C THR* 1.3 61.4 + - - +
257C ASN* 3.5 23.0 + - + +
258C THR 3.4 14.9 + - - +
259C LEU 3.5 11.4 - - - +
260C THR* 3.3 41.7 - - + +
261C THR* 5.6 0.2 - - - -
305C TYR* 3.9 8.5 - - + +
306C PHE* 3.3 2.1 - - - -
307C LYS* 2.6 63.8 + - + +
266D GLU* 2.9 32.3 + - - -
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Residues in contact with THR 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C VAL* 4.0 3.5 + - + -
126C LYS* 1.3 77.2 - - - +
128C GLU* 1.3 63.6 + - - +
165C PHE* 4.1 27.8 - - + -
256C THR 4.7 5.2 - - - +
259C LEU 5.3 2.5 + - - +
261C THR* 5.9 1.3 + - - +
304C ARG* 2.9 39.3 - - - +
305C TYR* 2.4 24.2 + - - -
306C PHE* 3.9 10.9 - - - -
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Residues in contact with GLU 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C THR* 1.3 80.4 + - - +
129C VAL* 1.3 70.7 + - - +
130C VAL* 3.8 21.4 + - + +
254C GLN 4.1 7.4 - - - +
255C PHE* 4.1 7.2 - - - -
256C THR 3.0 40.1 + - - +
257C ASN* 3.4 4.7 + - - +
303C PRO 3.9 0.2 - - - +
304C ARG* 3.4 1.6 - - - +
305C TYR* 2.8 40.9 + - + +
229D PRO 4.3 0.5 - - - +
231D PRO* 4.1 9.2 - - + +
239D TYR* 2.7 35.3 + - - -
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Residues in contact with VAL 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C GLU* 1.3 79.7 - - - +
130C VAL* 1.3 67.1 + - - +
132C SER* 3.8 3.5 + - - -
163C HIS* 5.0 4.0 - - + +
253C LEU* 3.5 36.8 - - + +
254C GLN 5.4 0.2 - - - +
255C PHE* 4.0 5.4 - - - -
284C ASP* 3.5 32.5 - - + +
286C MET* 5.5 0.9 - - - -
302C LEU* 3.4 30.5 - - + +
303C PRO 3.3 11.9 - - - +
304C ARG* 3.7 25.1 - - + +
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Residues in contact with VAL 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLU* 3.8 26.7 - - - +
129C VAL* 1.3 83.4 - - - +
131C GLY* 1.3 61.5 + - - +
132C SER 3.5 1.3 - - - -
255C PHE* 3.7 10.1 - - + -
302C LEU* 3.5 6.2 - - - +
303C PRO* 3.0 44.5 + - + +
304C ARG* 5.5 0.7 - - - -
305C TYR* 5.6 3.6 - - + +
175D GLN* 6.5 0.7 - - + -
177D LEU* 3.6 9.8 - - + +
208D LEU* 4.8 9.9 - - + -
228D HIS* 5.1 4.3 - - + -
229D PRO 4.2 5.6 - - - +
230D ASP* 5.6 0.2 - - - -
231D PRO* 4.0 22.7 - - + -
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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