Contacts of the helix formed by residues 272 - 285 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C LYS* 2.6 20.6 + - - -
92C HIS* 2.5 35.1 + - + +
270C ASN 3.3 8.4 + - - +
271C ASP* 1.3 72.8 + - - +
273C GLU* 1.3 66.1 + - - +
275C PHE* 3.3 8.5 + - + +
276C SER* 2.8 31.5 + - - +
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Residues in contact with GLU 273 (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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445A GLN* 5.3 0.7 + - - -
271C ASP* 3.3 17.9 + - - +
272C GLU* 1.3 81.9 - - - +
274C MET* 1.3 62.4 + - - +
276C SER* 3.2 6.1 + - - -
277C ALA* 3.0 23.3 + - - +
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Residues in contact with MET 274 (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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106C LEU* 3.6 28.9 - - + -
109C LEU* 4.4 25.2 - - + +
110C ALA* 4.8 9.4 - - - -
210C LYS* 4.8 12.6 - - - +
212C PHE* 3.7 26.7 - - + -
269C MET* 3.4 31.3 - - + +
271C ASP* 3.0 28.8 + - + +
272C GLU 3.3 0.2 - - - -
273C GLU* 1.3 75.9 - - - +
275C PHE* 1.3 58.1 + - - +
277C ALA* 3.3 6.6 + - + +
278C ALA* 2.8 31.4 + - - +
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Residues in contact with PHE 275 (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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81C GLU* 6.1 0.9 - - - -
92C HIS* 3.5 53.2 - + + -
93C ILE 4.1 7.6 - - - -
94C VAL* 3.7 27.6 - - + -
269C MET* 3.8 11.8 - - - -
271C ASP 3.0 19.0 + - - +
272C GLU* 3.5 8.7 - - + +
273C GLU 3.2 0.2 - - - -
274C MET* 1.3 77.7 - - - +
276C SER* 1.3 65.3 + - - +
278C ALA* 3.4 1.2 + - - +
279C LYS* 3.1 59.8 + - + +
289C PRO* 5.9 1.1 - - + -
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Residues in contact with SER 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A GLN* 3.6 30.6 - - - +
272C GLU* 2.8 18.4 + - - +
273C GLU* 3.6 6.5 - - - -
275C PHE* 1.3 78.8 - - - +
277C ALA* 1.3 62.5 + - - +
279C LYS* 3.4 25.4 + - - +
280C GLU* 3.4 13.3 + - - +
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Residues in contact with ALA 277 (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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445A GLN* 4.2 10.7 - - - +
109C LEU* 3.5 21.9 - - + +
273C GLU 3.0 16.1 + - - +
274C MET* 3.8 4.7 - - - +
276C SER* 1.3 78.3 - - - +
278C ALA* 1.3 61.7 + - - +
280C GLU* 3.4 9.1 + - - +
281C LEU* 3.2 22.3 + - - +
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Residues in contact with ALA 278 (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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94C VAL* 4.5 9.9 - - + -
105C LEU* 4.7 3.9 - - + +
109C LEU* 3.5 24.2 - - + +
267C LEU* 4.2 10.3 - - + -
269C MET* 4.0 15.7 - - + -
274C MET 2.8 19.0 + - - +
275C PHE* 3.7 4.9 - - - +
277C ALA* 1.3 73.6 - - - +
279C LYS* 1.3 60.2 + - - +
281C LEU* 3.8 1.9 - - - +
282C VAL* 2.9 34.1 + - - +
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Residues in contact with LYS 279 (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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446A LEU* 4.3 10.3 - - + +
449A PHE* 4.9 17.7 - - - -
450A THR* 4.9 15.4 + - - +
94C VAL* 5.1 2.4 - - + +
275C PHE* 3.1 58.1 + - + +
276C SER* 3.5 18.7 + - - +
277C ALA 3.2 0.2 - - - -
278C ALA* 1.3 77.4 - - - +
280C GLU* 1.3 58.9 + - - +
282C VAL* 3.1 23.3 - - - +
283C VAL* 3.4 12.0 - - - +
289C PRO* 3.4 31.2 - - + +
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Residues in contact with GLU 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A GLN* 3.2 45.1 + - + +
446A LEU* 4.2 20.2 + - + +
276C SER 3.4 3.6 + - - +
277C ALA* 3.4 10.0 + - - +
278C ALA 3.3 0.4 - - - -
279C LYS* 1.3 79.8 - - - +
281C LEU* 1.3 62.6 + - + +
283C VAL* 3.7 14.9 - - - +
284C VAL* 4.5 6.2 + - - +
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Residues in contact with LEU 281 (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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128A PHE* 5.5 6.3 - - + -
105C LEU* 4.2 18.4 - - + +
108C GLN* 3.7 42.6 - - + +
109C LEU* 4.1 20.2 - - + -
277C ALA 3.2 15.6 + - - +
278C ALA* 3.3 5.4 + - - +
280C GLU* 1.3 78.3 - - + +
282C VAL* 1.3 63.7 + - - +
283C VAL 3.2 2.0 - - - -
284C VAL* 3.3 26.1 - - + +
285C TYR* 3.4 21.3 - - + -
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Residues in contact with VAL 282 (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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94C VAL* 4.0 16.6 - - + -
95C PRO 4.2 7.2 - - - +
105C LEU* 3.9 21.9 - - + +
278C ALA 2.9 15.6 + - - +
279C LYS* 3.1 19.7 - - - +
281C LEU* 1.3 76.5 - - - +
283C VAL* 1.3 63.6 + - - +
286C GLU* 2.8 53.2 + - + +
287C GLY 3.0 21.1 + - - +
288C MET 4.9 0.2 - - - +
289C PRO* 3.9 18.4 - - + -
292C GLY* 4.6 2.2 - - - -
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Residues in contact with VAL 283 (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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100A ARG* 2.8 45.8 + - - +
125A THR* 5.2 3.1 - - + -
446A LEU* 3.8 28.5 - - + -
448A PHE* 6.2 2.2 - - + -
279C LYS 3.4 18.6 - - - +
280C GLU 3.7 10.8 - - - +
281C LEU 3.2 0.4 - - - -
282C VAL* 1.3 81.0 - - - +
284C VAL* 1.3 65.2 + - + +
285C TYR 3.5 0.2 + - - -
287C GLY 3.4 9.2 + - - -
288C MET* 4.3 17.3 - - - -
289C PRO* 4.4 5.6 - - + -
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Residues in contact with VAL 284 (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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100A ARG* 3.6 12.6 - - - +
124A THR 5.5 0.7 - - - +
125A THR* 4.5 12.3 - - + -
128A PHE* 3.6 57.0 - - + -
129A HIS* 2.8 26.4 + - - +
280C GLU 4.9 4.0 - - - +
281C LEU* 3.3 23.3 - - + +
283C VAL* 1.3 85.3 - - + +
285C TYR* 1.3 71.2 + - + +
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Residues in contact with TYR 285 (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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97A HIS* 3.3 18.7 - - - -
100A ARG* 4.5 3.3 - - - +
101A GLY* 4.5 11.4 + - - -
104A ASN* 4.0 24.5 - - + -
108A GLN* 5.5 0.6 + - - -
128A PHE* 4.5 5.9 - + - -
129A HIS* 3.9 19.3 - + - -
132A LYS* 3.6 21.6 - - - +
285A TYR* 4.7 6.5 - + - -
286A GLU* 4.7 1.6 - - - +
104C ASN* 3.5 27.4 - - - +
105C LEU* 4.3 6.7 - - + -
108C GLN* 3.4 33.8 + - - -
281C LEU* 3.4 27.8 - - + +
282C VAL 3.2 1.8 + - - +
284C VAL* 1.3 95.6 - - + +
286C GLU* 1.3 72.4 + - + +
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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