Contacts of the helix formed by residues 303 - 313 (chain C) in PDB entry 1FBA
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 ARG 303 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C GLU* 5.0 4.1 + - - +
42C ARG* 3.5 50.9 - - - +
45C ASP* 5.3 4.0 + - - -
271C SER* 5.1 3.0 + - - +
272C GLY 5.0 7.6 - - - -
302C GLY* 1.3 72.2 - - - +
304C ALA* 1.3 57.0 - - - +
305C LEU 3.1 0.2 + - - -
306C GLN* 3.0 5.7 + - - +
307C ALA* 2.8 40.8 + - - +
310C LEU* 6.3 0.2 - - - +
356C LEU* 3.2 57.8 + - + +
358C VAL* 4.2 15.7 - - - +
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Residues in contact with ALA 304 (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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271C SER* 3.3 33.5 + - - +
274C GLN 4.9 0.2 - - - +
276C GLU* 3.5 24.4 - - - +
279C ALA* 4.2 9.9 - - + -
301C TYR* 3.8 19.7 - - + -
302C GLY 3.1 0.6 - - - -
303C ARG* 1.3 79.3 - - - +
305C LEU* 1.3 58.8 + - - +
330C ARG* 4.2 9.4 - - - +
334C ASN* 4.6 3.3 + - - -
356C LEU* 4.0 15.9 - - + +
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Residues in contact with LEU 305 (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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29C ILE 3.9 14.8 - - - +
30C LEU* 3.7 28.5 - - + -
73C ILE* 4.1 9.9 - - + -
276C GLU* 4.3 4.3 - - - +
299C PHE* 3.9 15.5 - - + -
301C TYR* 3.9 21.7 - - + +
302C GLY 3.1 8.5 + - - +
303C ARG 3.0 0.6 - - - -
304C ALA* 1.3 77.4 - - - +
306C GLN* 1.3 60.7 + - - +
307C ALA 3.8 0.7 - - - -
309C VAL* 3.7 14.6 - - - +
326C GLU 5.1 0.2 - - - +
327C LEU* 4.1 11.8 - - + +
330C ARG* 3.7 45.8 - - + +
331C ALA* 3.8 10.8 - - + +
334C ASN* 4.0 8.1 - - - +
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Residues in contact with GLN 306 (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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30C LEU* 4.3 13.4 - - + +
31C ALA 3.0 28.9 + - - -
32C ALA* 4.2 3.0 - - - +
34C GLU* 3.2 25.1 + - - +
39C MET* 5.1 0.5 - - - +
58C TYR* 3.0 38.7 + - - +
62C LEU* 3.8 18.0 - - + +
302C GLY 3.2 18.0 + - - +
303C ARG* 3.0 3.2 + - - +
305C LEU* 1.3 81.2 - - - +
307C ALA* 1.3 66.8 + - - +
308C SER 3.3 2.5 - - - -
309C VAL* 3.0 18.2 + - - +
310C LEU* 3.1 22.5 + - + +
327C LEU* 5.8 0.7 - - + -
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Residues in contact with ALA 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C GLU* 3.3 19.6 + - - +
303C ARG* 2.8 25.3 + - - +
306C GLN* 1.3 73.0 - - - +
308C SER* 1.3 61.9 + - - +
310C LEU* 3.7 7.3 + - - +
311C ARG* 3.4 19.2 + - - +
353C SER* 3.7 9.2 - - - +
356C LEU* 3.6 26.7 - - + -
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Residues in contact with SER 308 (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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276C GLU* 2.7 32.7 + - - -
307C ALA* 1.3 74.7 - - - +
309C VAL* 1.3 61.2 + - - +
311C ARG* 3.4 13.2 + - - +
312C ALA* 2.9 31.0 + - - +
326C GLU* 3.7 27.6 - - - +
330C ARG* 5.8 2.7 - - - -
352C GLY* 4.2 8.3 - - - -
353C SER* 4.2 2.6 + - - -
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Residues in contact with VAL 309 (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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58C TYR* 3.8 16.6 - - + +
61C LEU* 3.8 29.2 - - + -
62C LEU* 3.9 6.3 - - + -
305C LEU 3.7 20.9 - - - +
306C GLN* 3.0 10.7 + - - +
308C SER* 1.3 74.8 - - - +
310C LEU* 1.3 56.8 + - - +
312C ALA* 3.0 4.5 + - - +
313C TRP* 2.8 35.0 + - - +
323C GLY* 3.7 14.9 - - - +
326C GLU* 4.1 3.1 - - + -
327C LEU* 3.6 37.2 - - + +
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Residues in contact with LEU 310 (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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39C MET* 4.3 3.6 - - + -
42C ARG* 3.8 32.8 - - + +
43C LEU* 3.8 20.0 - - + -
46C ILE* 3.6 42.5 - - + +
58C TYR* 3.6 38.1 - - + +
303C ARG* 6.3 0.7 - - - +
306C GLN* 3.1 17.1 + - + +
307C ALA* 4.0 6.7 - - - +
309C VAL* 1.3 78.0 - - - +
311C ARG* 1.3 57.3 + - - +
313C TRP* 3.3 4.3 + - + +
314C ALA* 2.8 30.7 + - - -
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Residues in contact with ARG 311 (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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46C ILE* 4.5 6.4 - - - +
307C ALA 3.4 11.8 + - - +
308C SER* 3.6 16.3 + - - +
309C VAL 3.2 0.4 - - - -
310C LEU* 1.3 80.8 - - - +
312C ALA* 1.3 63.2 + - - +
314C ALA* 3.8 13.0 + - - +
352C GLY 5.0 9.7 + - - -
353C SER* 5.5 7.1 - - - +
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Residues in contact with ALA 312 (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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308C SER 2.9 18.2 + - - +
309C VAL 3.4 3.8 - - - +
311C ARG* 1.3 79.2 - - - +
313C TRP* 1.3 65.5 + - - +
314C ALA* 4.4 0.7 - - - +
319C ASN* 3.2 20.5 - - - +
322C ALA* 4.0 9.2 - - + +
323C GLY* 3.8 20.9 - - - +
326C GLU* 3.8 14.6 - - + +
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Residues in contact with TRP 313 (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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43C LEU* 4.1 9.0 - - + -
46C ILE* 3.7 28.0 - - + -
48C VAL* 4.7 10.1 - - + -
54C ASN* 4.2 8.1 - - - -
57C ALA* 4.5 10.5 - - + -
58C TYR* 3.5 54.3 - + + -
61C LEU* 3.4 32.7 - - + +
309C VAL 2.8 16.6 + - - +
310C LEU* 3.6 4.3 - - + +
312C ALA* 1.3 72.4 - - - +
314C ALA* 1.3 65.4 + - - +
315C GLY* 3.0 33.6 + - - -
316C LYS 3.3 30.9 + - - -
317C LYS* 4.9 3.7 - - + +
319C ASN* 3.0 27.4 - - - +
320C ILE* 4.5 12.0 - - - +
323C GLY* 4.5 1.7 - - - -
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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