Contacts of the helix formed by residues 12 - 24 (chain C) in PDB entry 3IFA
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 THR 12 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C MET 2.7 10.2 + - - +
11C LEU* 1.3 90.6 - - + +
13C LEU* 1.3 59.1 + - - +
14C THR* 3.7 2.3 + - - -
15C ARG* 3.2 28.8 + - - +
16C TYR* 2.9 31.2 + - - +
184C PHE* 4.8 0.9 - - - -
190C LEU* 5.0 2.2 - - + -
192C GLU* 3.7 28.5 + - + +
193C PHE 3.3 8.7 - - - +
194C VAL* 5.5 0.2 - - + -
39D THR* 4.1 26.5 + - + +
84D MET* 4.9 5.4 - - + -
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Residues in contact with LEU 13 (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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11C LEU 4.1 0.4 + - - -
12C THR* 1.3 69.3 - - - +
14C THR* 1.3 60.4 + - - +
16C TYR* 4.2 0.7 - - + -
17C VAL* 2.9 53.5 + - + +
38C LEU* 3.3 42.0 - - + -
173C VAL* 4.4 7.0 - - + -
175C LEU* 4.2 6.5 - - + -
184C PHE* 3.5 48.0 - - + -
192C GLU* 5.8 0.2 - - - +
193C PHE* 2.9 46.0 + - + +
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Residues in contact with THR 14 (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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12C THR* 3.3 4.9 + - - -
13C LEU* 1.3 78.3 - - - +
15C ARG* 1.3 57.2 + - - +
17C VAL* 3.9 2.6 - - - +
18C MET* 3.1 27.3 + - + +
31C THR* 5.9 0.2 - - - +
35C ASN* 4.4 14.2 + - - +
38C LEU* 6.2 1.1 - - - -
192C GLU* 3.3 23.2 + - - +
14D THR* 3.8 33.8 + - + +
35D ASN* 4.1 24.2 - - + +
39D THR* 6.0 1.1 - - - -
192D GLU* 5.2 4.3 + - - -
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Residues in contact with ARG 15 (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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9C ASP 3.9 3.4 + - - -
10C MET* 2.9 45.9 + - + +
11C LEU* 4.4 3.6 - - - +
12C THR* 3.2 15.6 + - - +
14C THR* 1.3 74.8 - - - +
16C TYR* 1.3 61.0 + - - +
19C GLU* 2.9 27.5 + - - +
32D GLN* 2.9 35.2 + - - +
35D ASN* 4.4 11.4 - - + +
36D SER* 2.8 44.0 + - - +
39D THR* 5.6 1.8 - - - +
84D MET* 2.9 42.6 + - + +
87D SER* 2.8 29.0 + - - -
88D SER* 3.4 11.8 - - - +
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Residues in contact with TYR 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ASP* 4.3 19.3 - - - -
10C MET* 3.8 13.6 - - + +
11C LEU 5.7 0.9 - - - +
12C THR 2.9 17.8 + - - +
13C LEU* 3.7 7.6 - - - +
15C ARG* 1.3 76.7 - - - +
17C VAL* 1.3 62.1 + - + +
19C GLU* 3.3 2.8 + - - +
20C LYS* 2.9 64.3 + - + +
175C LEU* 5.9 3.4 - - + -
182C ASP* 2.7 37.5 + - + -
184C PHE* 3.7 20.9 - + + -
195C LEU* 4.1 25.8 - - + -
198C LYS* 3.4 25.3 + - - -
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Residues in contact with VAL 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 2.9 46.0 + - + +
14C THR* 3.9 4.3 - - - +
16C TYR* 1.3 73.8 - - + +
18C MET* 1.3 67.5 + - - +
20C LYS* 3.2 5.3 + - - +
21C GLY 3.0 6.2 + - - -
31C THR* 4.2 15.3 - - + +
34C LEU* 4.0 24.9 - - + -
35C ASN* 4.4 7.0 - - - +
38C LEU* 4.4 7.6 - - + -
175C LEU* 4.1 17.3 - - + -
339C AMP 2.9 38.2 + - - +
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Residues in contact with MET 18 (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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14C THR 3.1 20.0 + - - +
15C ARG 3.6 4.7 - - - +
16C TYR 3.3 0.2 - - - -
17C VAL* 1.3 75.3 - - - +
19C GLU* 1.3 57.6 + - - +
21C GLY* 3.1 4.3 + - - -
22C ARG* 3.0 37.3 + - + +
31C THR* 4.2 12.3 + - + -
18D MET* 3.6 35.7 - - + +
28D GLY* 3.5 33.7 - - - +
31D THR* 3.8 19.5 - - + -
32D GLN* 3.4 26.9 - - + +
35D ASN* 4.4 6.5 - - - +
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Residues in contact with GLU 19 (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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10C MET* 4.0 24.0 - - + +
15C ARG 2.9 18.6 + - - +
16C TYR 3.6 4.0 - - - +
17C VAL 3.2 0.2 - - - -
18C MET* 1.3 78.4 - - - +
20C LYS* 1.3 57.3 + - + +
22C ARG* 3.0 39.8 + - - +
23C GLN* 3.0 45.2 + - - +
32D GLN* 3.2 14.4 + - - +
88D SER 5.2 2.1 - - - +
89D TYR* 6.1 1.9 - - - +
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Residues in contact with LYS 20 (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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16C TYR* 2.9 57.1 + - + +
17C VAL* 3.2 4.2 + - - +
19C GLU* 1.3 76.0 - - + +
21C GLY* 1.3 56.9 + - - +
23C GLN* 3.4 32.9 + - - +
24C ALA* 3.0 28.4 + - - +
177C THR* 3.5 9.9 + - - +
179C GLN* 3.0 38.4 + - - +
182C ASP* 5.2 2.6 + - - -
339C AMP 3.4 23.5 + - - +
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Residues in contact with GLY 21 (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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17C VAL 3.0 9.5 + - - -
18C MET 3.1 5.6 + - - -
20C LYS* 1.3 76.0 - - - +
22C ARG* 1.3 62.2 + - - +
24C ALA 3.4 0.7 + - - -
25C LYS 3.2 2.9 + - - -
26C GLY* 3.0 30.6 + - - +
31C THR* 3.9 5.6 - - - -
339C AMP 3.4 30.0 + - - -
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Residues in contact with ARG 22 (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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18C MET* 3.0 36.8 + - + +
19C GLU* 3.0 40.2 + - - +
21C GLY* 1.3 72.7 - - - +
23C GLN* 1.3 64.5 + - - +
25C LYS* 3.0 18.5 + - - +
27D THR* 3.1 33.5 + - - +
28D GLY 3.9 14.6 + - - -
29D GLU* 3.9 24.7 + - - +
32D GLN* 3.8 13.5 - - - +
88D SER 4.9 5.7 + - - -
89D TYR* 5.8 3.4 - - - +
90D SER* 4.9 1.4 + - - -
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Residues in contact with GLN 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLU* 3.0 35.1 + - - +
20C LYS* 3.6 39.8 - - - +
22C ARG* 1.3 77.6 - - - +
24C ALA* 1.3 60.9 + - - +
25C LYS* 3.3 11.1 + - - +
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Residues in contact with ALA 24 (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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20C LYS 3.0 17.8 + - - +
21C GLY 3.7 4.7 - - - +
22C ARG 3.2 0.2 - - - -
23C GLN* 1.3 74.9 - - - +
25C LYS* 1.3 67.7 + - - +
26C GLY 3.4 0.3 + - - -
339C AMP 3.5 44.3 - - + +
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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