Contacts of the helix formed by residues 303 - 320 (chain B) in PDB entry 1G5J
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 TRP 303 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A GLN* 4.4 29.0 + - - +
116A LEU* 5.0 1.6 - - - +
301B ASN* 4.3 3.2 + - - +
302B LEU* 1.3 74.2 - - - +
304B ALA* 1.3 73.9 + - - +
306B GLN* 4.2 1.2 - - - +
307B ARG* 3.3 55.4 + - + +
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.7 3.1 - - + +
115A GLN* 3.9 18.4 - - + +
116A LEU* 3.2 36.0 - - + +
302B LEU* 3.6 1.4 - - - +
303B TRP* 1.3 91.7 - - - +
305B ALA* 1.4 57.7 + - - +
306B GLN 2.5 16.4 + - - -
307B ARG* 2.6 9.4 + - - -
308B TYR* 2.7 22.6 + - + +
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 4.6 1.4 - - - +
126A SER* 3.2 35.2 - - - +
129A GLN* 3.3 10.8 - - + -
130A VAL* 3.2 23.5 - - + -
302B LEU* 3.5 20.9 - - + +
304B ALA* 1.4 72.9 - - - +
306B GLN* 1.3 66.3 + - - +
308B TYR* 3.3 10.1 - - - +
309B GLY 2.8 19.9 + - - -
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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
----------------------------------------------------------
129A GLN* 3.4 27.8 + - - +
133A GLU* 3.7 28.0 + - + +
302B LEU 4.1 16.6 + - - +
303B TRP 4.2 1.1 - - - +
304B ALA 2.5 4.7 + - - +
305B ALA* 1.3 81.3 - - - +
307B ARG* 1.3 65.4 + - - +
310B ARG* 3.3 16.0 + - - +
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Residues in contact with ARG 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B TRP* 3.3 54.0 + - + +
304B ALA* 2.6 7.0 + - - -
306B GLN* 1.3 77.1 + - - +
308B TYR* 1.3 66.5 + - - +
310B ARG* 2.8 26.6 + - + +
311B GLU* 2.9 30.3 + - - +
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Residues in contact with TYR 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA* 3.7 20.3 + - + -
109A PHE* 4.7 7.7 - + - -
112A LEU* 2.7 55.5 - - + +
116A LEU* 5.2 2.0 - - + -
130A VAL* 4.7 1.8 - - + -
150A PHE* 3.0 52.3 + + - -
154A LEU* 4.2 7.6 - - + -
304B ALA* 2.7 36.9 + - + +
305B ALA* 3.3 13.5 - - - +
307B ARG* 1.3 71.6 - - - +
309B GLY* 1.3 61.4 + - - +
311B GLU* 3.7 8.2 + - + +
312B LEU* 3.3 24.6 + - + +
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Residues in contact with GLY 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL* 3.9 24.6 - - - +
133A GLU* 4.3 7.2 - - - -
134A LEU* 4.0 7.4 - - - +
150A PHE* 4.7 0.7 - - - -
305B ALA 2.8 20.9 + - - -
306B GLN 4.0 0.7 - - - -
308B TYR* 1.3 71.3 - - - +
310B ARG* 1.3 59.8 + - - +
312B LEU* 3.1 8.2 + - - +
313B ARG* 2.8 29.3 + - - +
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Residues in contact with ARG 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLU* 4.1 15.9 - - + +
306B GLN 3.3 13.4 + - - +
307B ARG* 2.8 19.7 + - + +
309B GLY* 1.3 74.4 - - - +
311B GLU* 1.3 62.5 + - - +
313B ARG* 2.9 33.0 + - + +
314B ARG* 3.3 7.1 + - - +
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Residues in contact with GLU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA* 5.7 7.5 - - + +
307B ARG* 2.9 29.6 + - + +
308B TYR* 3.9 7.1 - - + +
310B ARG* 1.3 77.2 - - - +
312B LEU* 1.3 64.3 + - + +
313B ARG 3.3 0.7 + - - -
314B ARG* 3.4 14.2 + - + +
315B MET* 3.4 35.9 + - + +
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Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PHE* 3.0 50.4 - - + -
108A ALA* 3.9 26.2 - - + -
109A PHE* 5.2 8.7 - - + -
134A LEU* 3.9 15.3 - - + -
146A ALA* 3.8 17.5 - - + +
150A PHE* 3.5 30.7 - - + -
308B TYR* 3.3 14.3 + - + +
309B GLY 3.1 9.3 + - - +
311B GLU* 1.3 80.1 - - - +
313B ARG* 1.3 62.5 + - - +
315B MET* 3.6 1.5 + - - -
316B SER* 3.2 18.1 + - - -
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Residues in contact with ARG 313 (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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133A GLU 4.0 17.8 + - - +
134A LEU* 4.1 10.5 - - - +
136A ARG* 6.0 3.7 - - - +
137A ASP* 4.6 24.5 + - - +
143A ARG* 3.4 26.6 - - - +
309B GLY 2.8 12.1 + - - +
310B ARG* 2.9 21.8 + - - +
312B LEU* 1.3 74.5 - - - +
314B ARG* 1.3 70.7 + - - +
316B SER* 2.7 28.8 + - - -
317B ASP* 3.1 6.3 + - - +
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Residues in contact with ARG 314 (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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310B ARG 3.3 6.8 + - - +
311B GLU* 3.4 11.2 + - + +
313B ARG* 1.3 81.5 - - - +
315B MET* 1.3 69.2 + - + +
317B ASP* 2.9 21.9 + - + +
318B GLU* 3.3 10.4 + - - +
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Residues in contact with MET 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PHE* 3.1 39.2 - - + -
104A ARG* 5.4 7.5 - - + -
105A TYR* 3.6 48.7 - - + +
108A ALA* 4.9 7.4 - - + -
311B GLU* 3.4 40.4 + - + +
312B LEU* 3.8 6.3 - - - +
313B ARG 3.3 0.6 - - - -
314B ARG* 1.3 81.0 - - + +
316B SER* 1.3 49.6 + - - +
318B GLU* 3.4 8.0 + - - +
319B PHE* 2.6 35.2 + - - +
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Residues in contact with SER 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PHE* 3.9 7.4 - - - -
134A LEU* 5.6 1.6 - - - -
143A ARG* 3.0 52.6 + - - -
146A ALA* 5.8 0.2 - - - -
312B LEU* 3.2 12.7 + - - -
313B ARG* 2.7 16.6 + - - -
315B MET* 1.3 75.0 - - - +
317B ASP* 1.3 68.4 + - - +
319B PHE* 2.8 26.1 + - - +
320B VAL* 3.2 12.0 + - - +
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Residues in contact with ASP 317 (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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143A ARG* 4.9 11.9 + - - +
313B ARG* 3.1 7.7 + - - +
314B ARG* 2.9 13.5 + - + +
316B SER* 1.3 81.9 + - - +
318B GLU* 1.3 58.3 + - + +
320B VAL* 2.8 24.6 - - - +
321B ASP* 4.8 3.3 - - - +
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Residues in contact with GLU 318 (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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104A ARG* 3.9 30.6 + - - +
105A TYR* 5.7 5.2 - - - -
314B ARG 3.3 7.3 + - - +
315B MET* 3.8 9.4 - - - +
316B SER 3.1 0.4 - - - -
317B ASP* 1.3 75.6 - - + +
319B PHE* 1.3 67.8 + - - +
320B VAL 3.0 9.3 + - - +
321B ASP* 4.6 5.8 - - - +
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Residues in contact with PHE 319 (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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97A ALA* 3.1 43.3 - - + -
100A GLU* 3.8 17.7 - - + -
101A PHE* 3.8 31.4 - + + -
104A ARG* 4.7 20.6 + - - +
142A GLY* 3.3 40.2 - - - -
145A VAL* 4.0 13.0 - - + -
146A ALA 4.5 0.9 - - - -
199A TYR* 4.9 3.6 - + - -
207A SER* 4.8 6.0 + - - -
315B MET 2.6 21.6 + - - +
316B SER* 2.8 16.9 + - - +
318B GLU* 1.3 74.2 - - - +
320B VAL* 1.3 55.9 + - + +
321B ASP 4.4 0.2 + - - -
323B PHE* 4.5 18.4 - + - -
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Residues in contact with VAL 320 (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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140A ASN* 5.2 13.0 - - + +
142A GLY* 3.4 23.8 - - - +
143A ARG* 6.2 1.3 - - - +
199A TYR* 2.8 33.2 - - + +
316B SER 3.2 10.6 + - - +
317B ASP* 2.8 24.8 - - - +
318B GLU 3.5 1.6 - - - +
319B PHE* 1.3 79.4 - - - +
321B ASP* 1.3 71.5 + - - +
323B PHE* 5.1 3.8 - - + -
324B LYS* 3.6 27.6 - - + +
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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
------------------------------------------------------------
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