Contacts of the helix formed by residues 293 - 309 (chain B) in PDB entry 1LBI
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 PHE 293 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B ALA* 4.0 13.9 - - + -
78B GLN* 3.9 39.9 - - + +
79B ILE* 3.2 42.1 - - + -
82B ALA* 3.0 13.5 - - - +
161B PHE* 4.1 11.0 - + - -
274B ASP* 3.6 41.5 - - + -
275B ASP 4.5 2.5 - - - -
276B THR* 4.5 7.6 - - + -
290B LYS* 5.5 2.4 - - - +
291B GLN* 3.0 38.1 + - + -
292B ASP* 1.3 70.9 + - - +
294B ARG* 1.3 61.6 + - + +
296B LEU* 3.6 5.7 - - - +
297B GLY 2.9 21.3 + - - -
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Residues in contact with ARG 294 (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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78B GLN 6.1 0.2 - - - +
81B ALA* 4.7 2.8 + - - +
82B ALA* 4.0 21.3 + - + +
85B SER* 3.4 37.1 + - - -
89B GLN* 5.1 8.9 - - - +
292B ASP* 3.6 11.9 - - - +
293B PHE* 1.3 74.2 - - + +
295B LEU* 1.3 65.9 + - - +
297B GLY* 3.5 1.4 + - - -
298B GLN* 3.2 23.3 + - - +
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Residues in contact with LEU 295 (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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161B PHE* 5.1 0.9 - - + -
292B ASP* 3.5 31.4 + - + +
294B ARG* 1.3 78.4 - - - +
296B LEU* 1.3 63.1 + - - +
298B GLN* 3.4 20.3 + - - +
299B THR* 2.9 53.0 + - - +
319B LEU* 3.5 27.8 - - + -
320B PRO* 4.7 13.2 - - + +
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Residues in contact with LEU 296 (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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79B ILE* 3.7 45.3 - - + -
148B LEU* 3.9 20.0 - - + +
159B ILE* 4.0 33.2 - - + +
161B PHE* 3.5 26.0 - - + -
292B ASP 2.9 18.4 + - - +
293B PHE* 3.7 4.7 - - - +
295B LEU* 1.3 76.3 - - - +
297B GLY* 1.3 53.9 + - - +
299B THR* 3.8 1.1 - - - -
300B SER* 2.5 38.0 + - - +
319B LEU* 3.7 13.5 - - + -
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Residues in contact with GLY 297 (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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79B ILE 4.5 1.6 - - - -
82B ALA* 3.9 20.9 - - - -
83B ILE* 4.0 13.4 - - - -
293B PHE 2.9 18.2 + - - -
295B LEU 3.3 0.2 - - - -
296B LEU* 1.3 78.3 - - - +
298B GLN* 1.3 59.0 + - - +
300B SER* 2.9 15.6 + - - -
301B VAL* 3.1 22.4 + - - +
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Residues in contact with GLN 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ALA 4.8 0.4 + - - -
86B ARG* 3.3 45.4 - - + +
294B ARG 3.2 15.6 + - - +
295B LEU* 3.5 21.2 - - - +
296B LEU 3.2 0.2 - - - -
297B GLY* 1.3 71.6 - - - +
299B THR* 1.3 82.1 + - - +
300B SER 2.8 3.2 + - - -
301B VAL* 3.0 13.0 + - - +
302B ASP* 3.0 19.6 + - - +
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Residues in contact with THR 299 (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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159B ILE* 3.3 30.5 - - + -
295B LEU* 2.9 40.4 + - - +
296B LEU* 3.8 5.4 - - - -
298B GLN* 1.3 85.9 + - - +
300B SER* 1.3 56.6 + - - +
302B ASP* 3.8 5.3 - - - +
303B ARG* 3.0 26.6 + - + +
317B GLN* 4.4 7.6 - - - +
319B LEU* 4.3 9.5 - - + +
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Residues in contact with SER 300 (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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83B ILE* 4.4 3.5 - - - +
123B ILE* 4.7 6.7 - - - -
146B LEU* 3.2 21.6 - - - +
148B LEU* 4.0 25.9 - - - +
159B ILE* 4.7 2.7 - - - -
296B LEU* 2.5 30.8 + - - +
297B GLY* 2.9 16.1 + - - -
298B GLN 2.8 3.4 + - - -
299B THR* 1.3 71.2 - - - +
301B VAL* 1.3 64.5 + - - +
302B ASP 3.0 1.1 - - - -
304B LEU* 2.9 26.4 + - - +
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 4.1 19.1 - - + -
83B ILE* 3.8 38.1 - - + +
86B ARG* 4.0 12.8 - - + -
87B ALA* 4.5 4.9 - - - +
90B LEU* 3.9 10.3 - - + -
92B ALA* 5.7 1.3 - - + -
123B ILE* 4.4 6.0 - - + +
297B GLY 3.1 19.0 + - - +
298B GLN 3.0 4.1 + - - +
300B SER* 1.3 77.3 - - - +
302B ASP* 1.3 72.0 + - - +
304B LEU* 3.1 20.1 - - - +
305B LEU* 3.1 24.7 + - + +
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Residues in contact with ASP 302 (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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86B ARG* 2.6 42.5 + - - -
90B LEU* 3.9 9.2 - - - +
298B GLN* 3.0 22.2 + - - +
299B THR* 3.8 6.3 - - - +
301B VAL* 1.3 81.9 - - - +
303B ARG* 1.3 60.6 + - - +
305B LEU* 3.3 17.3 + - - +
306B GLN* 3.4 27.5 + - - +
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Residues in contact with ARG 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU* 3.5 19.2 - - + +
157B ASN* 3.5 29.6 - - - +
158B SER 2.8 26.8 + - - -
159B ILE* 4.3 8.3 - - - -
299B THR 3.0 20.1 + - - +
302B ASP* 1.3 72.2 - - - +
304B LEU* 1.3 66.0 + - - +
306B GLN* 3.1 25.0 + - + +
307B LEU* 3.3 19.1 + - + +
313B VAL 3.6 22.1 + - - -
314B LYS* 4.0 0.8 - - - -
315B GLY* 3.4 26.2 + - - +
316B ASN 3.8 3.4 - - - +
317B GLN* 2.8 44.5 - - - +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 3.8 22.7 - - + -
121B GLY* 3.6 30.5 - - - +
122B LEU 3.6 24.0 - - - +
123B ILE* 4.1 14.4 - - + -
144B PRO* 4.0 15.7 - - + +
145B ALA 4.3 1.8 - - - -
146B LEU* 3.8 19.0 - - + +
300B SER 2.9 12.9 + - - +
301B VAL* 3.1 13.0 - - - +
303B ARG* 1.3 77.9 - - - +
305B LEU* 1.3 58.9 + - + +
307B LEU* 3.0 30.6 + - + +
308B SER* 3.7 6.6 + - - -
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Residues in contact with LEU 305 (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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62B LEU 5.7 7.2 - - - +
64B ILE* 5.2 13.2 - - + -
90B LEU* 3.2 35.0 - - + -
92B ALA* 5.6 5.8 - - + -
301B VAL* 3.1 27.0 + - + +
302B ASP* 3.6 11.7 - - - +
303B ARG 3.2 0.4 - - - -
304B LEU* 1.3 79.1 - - + +
306B GLN* 1.3 58.9 + - + +
307B LEU 3.1 4.9 - - - -
308B SER* 4.2 6.1 - - - +
309B GLN* 2.9 42.5 + - + +
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Residues in contact with GLN 306 (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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302B ASP* 3.4 26.3 + - - +
303B ARG* 3.1 20.3 + - + +
305B LEU* 1.3 76.2 - - + +
307B LEU* 1.3 64.9 + - - +
309B GLN 4.7 0.4 - - - -
310B GLY* 4.1 10.5 - - - +
311B GLN 3.2 35.9 + - - +
312B ALA* 4.6 0.2 - - - -
313B VAL* 6.2 0.3 - - - +
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Residues in contact with LEU 307 (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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144B PRO* 3.5 20.6 - - + -
145B ALA 3.8 16.4 - - - +
146B LEU* 3.3 33.4 - - + -
157B ASN* 3.3 25.8 - - + +
303B ARG* 3.4 18.4 - - + +
304B LEU* 3.0 17.5 + - + +
306B GLN* 1.3 83.8 - - - +
308B SER* 1.3 64.9 + - - +
310B GLY 3.3 7.3 - - - +
312B ALA* 3.4 37.6 + - + +
313B VAL 4.9 1.3 - - - +
314B LYS* 5.4 0.9 - - - +
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Residues in contact with SER 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B SER* 4.2 12.3 + - - -
142B ASN* 5.6 4.3 - - - +
144B PRO* 3.7 24.9 - - - +
304B LEU 3.9 6.2 + - - -
305B LEU* 3.6 9.9 + - - +
307B LEU* 1.3 78.3 - - - +
309B GLN* 1.3 64.5 + - - +
310B GLY 2.9 14.9 + - - +
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Residues in contact with GLN 309 (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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305B LEU* 2.9 25.6 + - + +
306B GLN* 4.7 0.7 - - - -
308B SER* 1.3 77.8 + - - +
310B GLY* 1.3 54.6 + - - +
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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