Contacts of the helix formed by residues 272 - 285 (chain B) in PDB entry 1C7G
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 GLU 272 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B LYS* 2.6 23.9 + - - -
92B HIS* 2.6 37.6 + - + +
270B ASN 3.3 10.1 + - - +
271B ASP* 1.3 73.6 + - - +
273B GLU* 1.3 64.1 + - - +
275B PHE* 3.6 5.3 - - + +
276B SER* 2.7 35.5 + - - +
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Residues in contact with GLU 273 (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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271B ASP* 3.3 17.4 - - - +
272B GLU* 1.3 81.3 + - - +
274B MET* 1.3 64.3 + - - +
276B SER* 3.4 6.2 + - - -
277B ALA* 3.1 22.7 + - - +
445D GLN* 5.5 0.5 + - - -
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Residues in contact with MET 274 (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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106B LEU* 3.6 28.9 - - + -
109B LEU* 4.5 25.3 - - + +
110B ALA* 5.3 5.8 - - + -
210B LYS* 4.8 9.0 - - - +
212B PHE* 3.6 26.2 - - + -
249B ASP 6.0 0.2 - - - +
267B LEU* 5.3 0.2 - - + -
269B MET* 3.3 37.6 - - + +
271B ASP* 3.0 33.8 + - + +
273B GLU* 1.3 75.1 - - - +
275B PHE* 1.3 60.1 + - - +
277B ALA* 3.2 7.0 + - - +
278B ALA* 2.8 31.4 + - - +
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Residues in contact with PHE 275 (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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81B GLU* 6.1 0.7 - - - -
92B HIS* 3.2 53.6 - + + -
93B ILE 4.2 8.1 - - - -
94B VAL* 3.8 26.9 - - + -
269B MET* 3.9 12.0 - - - +
271B ASP 3.0 17.6 + - - +
272B GLU* 3.6 8.3 - - + +
274B MET* 1.3 77.8 - - - +
276B SER* 1.3 58.9 + - - +
278B ALA* 3.1 2.1 + - - +
279B LYS* 2.9 65.5 + - + +
289B PRO* 5.9 1.3 - - + -
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Residues in contact with SER 276 (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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272B GLU* 2.7 22.1 + - - +
273B GLU* 3.7 6.5 - - - -
274B MET 3.3 0.2 - - - -
275B PHE* 1.3 79.1 - - - +
277B ALA* 1.3 62.2 + - - +
279B LYS* 3.6 20.4 + - - +
280B GLU* 3.5 14.4 + - - +
445D GLN* 3.9 31.3 + - - +
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Residues in contact with ALA 277 (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 LEU* 3.6 21.4 - - + +
273B GLU 3.1 16.8 + - - +
274B MET* 3.7 5.6 - - - +
276B SER* 1.3 74.4 - - - +
278B ALA* 1.3 65.3 + - - +
280B GLU* 3.3 8.1 + - - +
281B LEU* 3.2 22.0 + - - +
445D GLN* 4.3 11.6 - - - +
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Residues in contact with ALA 278 (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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94B VAL* 4.3 11.2 - - + -
105B LEU* 4.8 4.2 - - + +
109B LEU* 3.7 23.3 - - + +
267B LEU* 4.2 8.7 - - + -
269B MET* 3.8 16.4 - - + -
274B MET 2.8 18.2 + - - +
275B PHE* 3.1 5.8 + - - +
277B ALA* 1.3 75.8 - - - +
279B LYS* 1.3 60.5 + - - +
281B LEU* 3.2 3.3 + - - +
282B VAL* 2.9 33.0 + - - +
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Residues in contact with LYS 279 (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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94B VAL* 5.0 2.2 - - + +
275B PHE* 2.9 60.6 + - + +
276B SER* 3.6 19.1 + - - +
277B ALA 3.2 0.2 - - - -
278B ALA* 1.3 77.4 - - - +
280B GLU* 1.3 58.7 - - - +
282B VAL* 3.0 25.0 - - - +
283B VAL* 3.2 11.4 - - - +
289B PRO* 3.5 32.9 - - + +
446D LEU* 4.9 9.6 - - + -
449D PHE* 5.3 11.2 - - - -
450D THR* 5.2 14.9 + - - +
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Residues in contact with GLU 280 (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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276B SER 3.5 7.9 + - - +
277B ALA* 3.3 10.8 + - - +
278B ALA 3.2 0.2 - - - -
279B LYS* 1.3 79.9 - - - +
281B LEU* 1.3 63.8 + - + +
283B VAL* 3.6 16.1 - - - +
284B VAL* 4.3 6.9 + - - +
444D LYS 5.4 0.2 - - - +
445D GLN* 3.1 44.4 + - + +
446D LEU* 4.4 19.2 + - + +
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Residues in contact with LEU 281 (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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105B LEU* 4.1 20.4 - - + +
108B GLN* 3.6 43.5 - - + +
109B LEU* 4.0 21.8 - - + -
277B ALA 3.2 12.4 + - - +
278B ALA* 3.2 6.1 + - - +
280B GLU* 1.3 77.6 - - + +
282B VAL* 1.3 65.2 + - - +
283B VAL 3.2 2.5 + - - -
284B VAL* 3.3 25.2 - - + +
285B TYR* 3.4 21.9 - - + -
128D PHE* 6.0 2.5 - - + -
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Residues in contact with VAL 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B VAL* 3.8 24.7 - - + -
95B PRO 4.2 6.1 - - - +
105B LEU* 4.0 15.8 - - + +
278B ALA 2.9 14.8 + - - +
279B LYS* 3.0 22.0 - - - +
281B LEU* 1.3 76.7 - - - +
283B VAL* 1.3 68.0 + - - +
285B TYR 3.0 0.7 + - - -
286B GLU* 2.9 47.6 + - + +
287B GLY 3.1 20.2 + - - +
288B MET 4.6 0.7 - - - +
289B PRO* 3.9 20.9 - - + -
292B GLY* 4.5 2.9 - - - -
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Residues in contact with VAL 283 (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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279B LYS 3.2 18.8 - - - +
280B GLU 3.6 10.8 - - - +
282B VAL* 1.3 82.5 - - + +
284B VAL* 1.3 66.1 + - + +
285B TYR 3.4 0.2 + - - -
287B GLY 3.5 9.2 + - - -
288B MET* 4.2 16.6 - - - -
289B PRO* 4.4 1.1 - - + -
100D ARG* 2.9 42.7 + - - +
125D THR* 4.6 2.2 - - + +
446D LEU* 3.6 32.8 - - + -
448D PHE* 6.0 2.7 - - + -
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Residues in contact with VAL 284 (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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280B GLU 4.8 3.8 - - - +
281B LEU* 3.3 23.8 + - + +
283B VAL* 1.3 84.3 - - + +
285B TYR* 1.3 78.3 + - + +
100D ARG* 4.1 10.5 - - - +
124D THR 6.2 0.2 - - - -
125D THR* 5.0 11.3 - - + -
128D PHE* 3.8 48.2 - - + -
129D HIS* 2.9 27.5 + - - -
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Residues in contact with TYR 285 (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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104B ASN* 3.8 24.0 - - - +
105B LEU* 4.4 4.3 - - + -
108B GLN* 3.3 33.7 + - - -
281B LEU* 3.4 31.9 - - + +
282B VAL 3.0 2.2 + - - +
283B VAL 4.7 0.2 - - - -
284B VAL* 1.3 96.3 - - + +
286B GLU* 1.3 74.0 + - + +
97D HIS* 3.5 17.3 - - - -
100D ARG* 4.5 10.5 - - - +
101D GLY* 4.7 3.6 + - - -
104D ASN* 4.0 27.8 - - + -
108D GLN* 5.7 0.2 - - - -
128D PHE* 4.5 5.6 - + - -
129D HIS* 4.0 13.2 - + - -
132D LYS* 3.6 21.7 - - - +
285D TYR* 4.8 9.6 - + - -
286D GLU* 5.1 0.9 - - - +
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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