Contacts of the strand formed by residues 116 - 130 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PRO* 3.4 35.9 - - + +
22A PRO* 3.6 13.9 - - - +
110B GLU* 5.1 0.3 - - - +
111B ASP* 3.1 32.1 + - + -
114B CYS* 3.5 13.2 - - + -
115B ASP* 1.3 80.6 - - - +
117B LEU* 1.3 60.7 + - - +
314B TRP* 3.2 14.0 - - + -
315B VAL 2.8 24.5 + - - -
316B LYS* 3.7 6.2 - - - -
317B ASN 4.0 1.1 - - - +
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ASN 3.8 11.0 - - - +
110B GLU* 4.5 11.0 - - + -
116B THR* 1.3 76.8 - - - +
118B GLN* 1.3 59.2 + - - +
119B MET* 4.5 11.7 - - + -
314B TRP* 3.1 9.0 - - - -
315B VAL* 2.6 67.9 + - + +
317B ASN* 4.0 22.4 - - + +
318B PRO* 4.9 3.6 - - + -
322F ALA* 4.6 9.2 - - + +
325F ILE* 3.6 30.5 - - + -
326F SER* 5.6 1.1 - - - +
329F PHE* 5.4 3.4 - - + -
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Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLY 4.7 2.6 + - - -
43B PRO* 4.9 7.8 - - - +
108B LEU* 3.3 46.1 + - + +
109B ASN* 3.3 32.8 + - - +
117B LEU* 1.3 80.1 - - - +
119B MET* 1.3 65.7 + - - +
276B GLU* 5.7 0.2 - - - +
312B LYS* 4.1 26.5 - - - +
313B ARG 3.0 17.5 - - - +
314B TRP* 3.3 37.0 + - + -
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Residues in contact with MET 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 4.0 7.9 - - - -
117B LEU* 4.5 11.0 - - + -
118B GLN* 1.3 79.0 - - - +
120B TRP* 1.3 61.3 + - - +
121B GLU* 3.3 5.0 + - - +
272B LEU* 4.3 25.6 - - + -
273B CYS 3.9 7.9 - - - +
274B LYS* 3.7 37.5 - - + +
275B GLY 5.3 0.2 - - - +
276B GLU* 5.1 7.6 - - - +
311B ARG 3.5 2.3 - - - +
312B LYS* 3.7 2.9 - - - -
313B ARG* 2.8 35.1 + - + +
315B VAL* 3.9 31.6 - - + -
318B PRO* 6.5 0.7 - - - -
329F PHE* 4.2 19.1 - - + -
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Residues in contact with TRP 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 5.4 5.8 - - + -
41B THR* 4.7 8.1 - - + -
45B SER 4.7 2.5 - - - -
47B THR* 3.8 22.9 - - - -
105B LEU* 3.1 46.8 - - + +
106B PRO* 2.9 39.8 + - + +
108B LEU* 3.1 25.2 - - + +
119B MET* 1.3 73.1 - - - +
121B GLU* 1.3 59.7 - - - +
122B ALA 4.0 0.2 - - - -
272B LEU* 3.2 1.4 - - - -
273B CYS* 2.6 51.7 + - + +
276B GLU* 4.3 10.0 + - + -
310B LEU* 4.2 15.5 - - + -
311B ARG* 3.6 16.4 - - - -
312B LYS* 3.7 37.0 - - + -
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B MET 4.3 0.9 - - - +
120B TRP* 1.3 72.0 - - - +
122B ALA* 1.3 68.4 + - - +
123B VAL* 3.7 2.9 - - - +
264B LEU* 3.7 4.2 - - - +
269B VAL 2.7 30.8 - - - +
271B PRO 3.0 14.1 - - - +
272B LEU* 4.1 11.9 - - + +
310B LEU* 3.0 4.2 - - - +
311B ARG* 2.8 78.7 + - + +
313B ARG* 2.6 46.0 + - + +
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B TRP 3.9 2.2 + - - -
121B GLU* 1.3 78.7 - - - +
123B VAL* 1.3 61.2 + - - +
167B VAL* 4.7 4.7 - - + -
263B LEU* 3.6 19.5 - - + -
270B GLY* 3.4 10.4 - - - -
271B PRO* 2.9 38.5 + - + +
273B CYS* 5.4 2.0 - - - -
278B LEU* 5.1 4.9 - - + -
308B ILE* 3.8 17.5 - - + -
310B LEU* 3.4 15.3 - - + +
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B VAL* 6.3 0.2 - - + -
121B GLU* 3.7 21.8 - - - +
122B ALA* 1.3 80.0 - - - +
124B SER* 1.3 64.3 + - - +
262B VAL* 3.1 11.0 - - + +
263B LEU* 2.5 34.0 + - - -
264B LEU* 3.1 25.1 + - + -
309B THR* 2.7 20.2 + - - +
310B LEU* 4.2 1.6 - - - -
311B ARG* 4.0 24.0 - - + +
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Residues in contact with SER 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B VAL* 1.3 83.4 - - - +
125B VAL* 1.3 68.1 + - - +
260B THR* 3.7 17.5 - - - +
261B THR 2.7 20.2 - - - -
262B VAL* 4.5 5.2 - - - -
263B LEU* 3.2 8.9 - - - +
308B ILE* 3.7 0.2 - - - -
309B THR* 2.7 45.5 + - - +
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B SER* 1.3 80.9 - - - +
126B LYS* 1.3 76.3 + - - +
127B THR* 4.1 5.4 + - + +
165B PHE* 5.1 9.6 - - + -
167B VAL* 4.5 11.0 - - + -
260B THR* 3.8 2.9 - - - +
261B THR* 2.7 36.6 + - + +
263B LEU* 3.1 34.3 - - + -
306B PHE* 4.5 11.4 - - + -
307B LYS 2.9 20.0 - - - +
308B ILE* 4.0 12.6 - - + -
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Residues in contact with LYS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B VAL* 1.3 81.8 - - - +
127B THR* 1.3 62.0 + - - +
256B THR 5.7 2.0 - - - +
257B ASN* 3.3 29.6 + - - +
258B THR* 3.6 12.0 + - - +
259B LEU 3.4 25.1 - - - +
260B THR* 3.5 24.2 - - + -
261B THR* 5.1 0.4 - - - -
305B TYR* 4.4 8.3 - - + -
307B LYS* 2.7 63.4 + - + +
266C GLU* 3.4 33.2 + - - +
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Residues in contact with THR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B VAL* 4.8 5.6 - - + +
126B LYS* 1.3 78.7 - - - +
128B GLU* 1.3 74.2 + - - +
165B PHE* 4.0 29.6 - - + -
256B THR 4.6 6.2 - - - +
259B LEU 4.6 3.2 + - - +
261B THR* 5.8 2.9 - - - +
304B ARG* 2.9 31.9 + - - +
305B TYR* 2.6 24.1 + - - -
306B PHE* 4.6 8.1 - - - -
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B THR* 1.3 85.3 + - - +
129B VAL* 1.3 72.2 + - - +
130B VAL* 3.7 9.8 + - + +
254B GLN 3.8 17.3 - - - +
255B PHE* 3.3 24.0 - - + -
256B THR 3.1 25.5 - - - +
257B ASN* 3.8 2.1 + - - -
304B ARG* 3.4 1.6 - - - +
305B TYR* 2.7 43.4 + - + +
229C PRO 4.3 0.3 - - - +
231C PRO* 4.2 11.2 - - + +
239C TYR* 2.6 31.8 + - - -
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B GLU* 1.3 78.3 - - - +
130B VAL* 1.3 65.9 + - - +
132B SER* 3.7 1.0 + - - -
163B HIS* 4.8 4.0 - - + +
253B LEU* 3.7 33.4 - - + +
255B PHE* 3.5 16.3 - - - -
284B ASP* 3.4 31.2 - - + +
286B MET* 5.4 0.4 - - - -
302B LEU* 3.3 33.4 - - + +
303B PRO 3.2 13.2 - - - +
304B ARG* 3.6 21.1 - - + +
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLU* 3.8 19.7 - - - +
129B VAL* 1.3 76.7 - - - +
131B GLY* 1.3 57.0 + - - +
132B SER 3.7 0.4 - - - -
255B PHE* 3.3 24.0 - - + -
302B LEU* 3.1 4.4 - - - +
303B PRO* 2.9 34.3 + - + +
304B ARG 5.3 0.2 - - - -
305B TYR* 4.8 6.7 - - + +
175C GLN* 6.1 2.9 - - + -
177C LEU* 2.7 25.8 - - + +
208C LEU* 5.4 7.9 - - + -
228C HIS* 4.4 7.2 - - + -
229C PRO 3.9 19.3 - - - +
230C ASP* 5.6 0.4 - - - -
231C PRO* 4.5 15.3 - - + -
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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