Contacts of the helix formed by residues 337 - 349 (chain A) in PDB entry 1C0F
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 TYR 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ASP* 6.2 0.2 - - - -
18A LYS* 3.9 22.9 - - + -
26A ALA* 5.3 4.5 - - + -
27A PRO* 3.7 34.3 - - + -
30A VAL* 4.1 27.3 - - + +
334A GLU* 2.8 15.6 + - + +
336A LYS* 1.3 123.3 + - + +
338A SER* 1.3 57.0 + - - -
339A VAL* 3.3 3.4 - - - -
340A TRP* 3.0 8.1 + - + +
341A ILE* 2.8 38.5 + - + +
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Residues in contact with SER 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A SER* 3.3 27.3 + - - -
144A ALA* 3.6 17.0 - - - +
298A VAL* 6.0 1.1 - - - +
299A LEU 5.0 0.3 + - - -
300A SER* 4.5 5.1 - - - -
332A PRO* 4.8 6.2 - - - +
334A GLU* 3.4 11.4 + - - -
335A ARG* 3.2 32.1 + - - +
336A LYS 3.6 0.2 - - - -
337A TYR* 1.3 73.9 - - - +
339A VAL* 1.3 68.2 + - - +
341A ILE* 3.3 4.7 + - - +
342A GLY* 2.9 20.4 + - - -
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Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASP* 3.5 33.0 - - - +
106A THR* 3.9 10.2 - - + +
137A GLN* 3.5 42.6 - - + +
140A LEU* 3.7 13.6 - - + +
141A SER* 3.2 18.6 - - - +
154A ASP* 4.3 7.9 - - - +
300A SER* 4.2 8.5 - - - +
336A LYS 5.4 0.6 + - - +
337A TYR* 3.3 1.0 - - - -
338A SER* 1.3 80.7 - - - +
340A TRP* 1.3 64.4 + - - +
342A GLY 3.3 0.2 + - - -
343A GLY* 3.0 17.8 + - - -
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Residues in contact with TRP 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 2.9 43.2 + - + +
11A ASP* 4.2 15.5 + - + +
18A LYS* 3.6 34.5 - - + -
19A ALA 3.7 0.2 - - - -
20A GLY* 3.4 28.7 - - - +
21A PHE 3.4 24.0 - - - -
24A ASP* 3.4 22.4 - - + -
25A ASP 4.0 1.6 - - - -
26A ALA* 3.2 28.0 - - - -
27A PRO* 3.4 27.6 - - + -
106A THR* 5.9 0.2 - - - -
337A TYR* 3.0 11.4 + - + +
339A VAL* 1.3 80.9 - - - +
341A ILE* 1.3 66.7 + - + +
343A GLY* 3.0 3.6 + - - -
344A SER* 3.0 28.6 + - - -
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Residues in contact with ILE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ASP 3.5 23.6 - - - +
26A ALA* 4.7 1.6 - - + -
144A ALA* 4.6 2.2 - - + -
334A GLU* 3.8 31.9 - - + -
337A TYR* 2.8 35.9 + - + +
338A SER* 3.9 4.9 - - - +
340A TRP* 1.3 84.2 - - + +
342A GLY* 1.3 63.0 + - - +
344A SER* 3.2 3.1 + - - -
345A ILE* 3.0 39.5 + - + +
73S GLN* 3.7 28.3 - - - +
127S PHE* 4.1 15.0 - - + -
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Residues in contact with GLY 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU* 3.5 30.9 - - - +
143A TYR* 5.0 3.5 - - - +
144A ALA* 3.9 11.1 - - - +
338A SER 2.9 11.1 + - - -
339A VAL 3.8 1.6 - - - -
341A ILE* 1.3 76.0 - - - +
343A GLY* 1.3 62.7 + - - +
345A ILE* 3.2 6.3 + - - +
346A LEU* 2.9 25.1 + - - +
81S ILE* 4.9 2.4 - - - +
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Residues in contact with GLY 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 3.8 16.6 - - - +
104A LEU* 4.1 8.6 - - - +
140A LEU* 3.9 20.2 - - - +
339A VAL 3.0 10.2 + - - -
340A TRP 3.0 8.2 + - - -
342A GLY* 1.3 75.7 - - - +
344A SER* 1.3 61.6 + - - +
346A LEU* 3.3 2.0 + - - +
347A ALA* 2.9 28.4 + - - +
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Residues in contact with SER 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 3.8 11.5 - - - +
22A ALA* 3.7 2.9 - - - +
23A GLY* 2.8 22.2 + - - -
24A ASP 2.6 22.8 + - - -
340A TRP* 3.0 36.5 + - - -
341A ILE* 3.5 8.1 - - - -
343A GLY* 1.3 76.5 - - - +
345A ILE* 1.3 56.9 + - - +
347A ALA 4.1 0.5 - - - -
348A SER* 2.7 32.7 + - - -
27S PHE* 4.8 0.4 - - - -
127S PHE* 4.3 3.5 - - - -
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Residues in contact with ILE 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A TYR 5.6 0.4 - - - -
144A ALA* 4.6 8.7 - - - -
341A ILE* 3.0 30.0 + - + +
342A GLY* 3.7 6.1 - - - +
344A SER* 1.3 72.8 - - - +
346A LEU* 1.3 67.9 + - - +
348A SER* 2.9 14.0 + - - -
349A LEU* 3.4 14.8 + - + +
27S PHE* 4.2 11.6 - - + -
73S GLN* 3.6 28.0 - - + +
74S ASP* 3.9 14.1 - - + +
77S GLY* 3.9 11.0 - - - -
78S ALA* 3.7 26.7 - - - +
81S ILE* 4.1 9.6 - - + -
127S PHE* 4.1 16.2 - - + -
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Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LEU* 4.0 13.2 - - + -
133A TYR* 4.3 13.0 - - + +
135A ALA* 4.6 2.0 - - + -
140A LEU* 3.9 22.7 - - + -
143A TYR* 5.0 9.4 - - + -
342A GLY 2.9 16.2 + - - +
343A GLY 3.8 2.9 - - - +
345A ILE* 1.3 77.3 - - - +
347A ALA* 1.3 63.0 - - - +
348A SER 3.1 1.0 + - - -
349A LEU* 3.2 17.4 + - + +
352A PHE* 3.3 53.3 - - + +
81S ILE* 3.8 39.2 - - + +
85S GLN* 4.8 2.5 - - - +
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Residues in contact with ALA 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ALA* 4.2 5.4 - - + +
9A VAL* 4.3 5.8 - - + -
22A ALA* 3.7 23.3 - - + +
104A LEU* 4.1 8.7 - - + +
343A GLY 2.9 17.5 + - - +
346A LEU* 1.3 77.8 - - - +
348A SER* 1.3 59.4 + - - +
349A LEU 3.4 1.3 + - - +
352A PHE* 3.8 17.3 - - - +
356A TRP* 4.1 28.0 - - + -
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Residues in contact with SER 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ALA* 3.5 5.0 - - - -
23A GLY* 3.0 25.5 + - - -
344A SER 2.7 21.4 + - - -
345A ILE 2.9 7.7 + - - -
347A ALA* 1.3 75.7 - - - +
349A LEU* 1.3 64.5 + - - +
350A SER* 3.6 0.9 + - - -
27S PHE* 3.3 40.7 - - - +
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A ILE* 3.4 17.0 - - + +
346A LEU* 3.2 16.3 + - + +
347A ALA 3.4 1.1 - - - +
348A SER* 1.3 78.5 - - - +
350A SER* 1.3 67.6 + - - +
351A THR* 3.8 20.4 - - - +
352A PHE* 3.1 18.1 + - + +
353A GLN* 4.4 3.8 + - - +
27S PHE* 3.6 13.7 - - + +
78S ALA* 3.5 31.4 - - + -
81S ILE* 3.5 40.4 - - + -
82S PHE* 3.9 16.6 - - + +
85S GLN* 4.4 3.4 - - - +
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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