Contacts of the helix formed by residues 3 - 19 (chain C) in PDB entry 1FIU
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 PRO 3 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158B PHE* 3.3 24.2 - - + +
159B LEU 3.4 22.4 - - - +
160B VAL* 3.9 5.6 - - - +
161B ASP* 3.7 31.9 - - - +
164B ILE* 4.2 2.0 - - + -
1C MET* 4.1 1.8 - - - +
2C GLN* 1.3 97.5 - - + +
4C LEU* 1.3 60.8 + - - +
5C PHE 3.2 0.4 - - - -
6C THR* 2.9 44.2 + - - +
7C GLN* 3.1 9.5 + - - +
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Residues in contact with LEU 4 (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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157B GLU* 3.4 32.5 - - + +
158B PHE* 2.8 21.2 + - + +
159B LEU* 3.9 19.3 - - + -
2C GLN 3.4 1.3 + - - +
3C PRO* 1.3 71.7 - - - +
5C PHE* 1.3 58.3 - - - +
7C GLN* 3.2 30.6 + - + +
8C GLU* 2.8 33.2 + - + +
83C LYS* 3.7 25.4 - - + -
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Residues in contact with PHE 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ILE* 5.5 0.2 - - + -
159B LEU* 3.0 37.1 + - + +
160B VAL* 3.5 20.6 - - + -
164B ILE* 4.0 16.1 - - + +
165B ALA* 4.6 1.1 - - + -
4C LEU* 1.3 80.9 - - + +
6C THR* 1.3 56.5 + - - +
8C GLU* 3.4 6.7 + - + +
9C ARG* 3.0 27.4 + - - +
76C PHE* 4.7 4.6 - + + -
80C ALA* 3.6 44.4 - - + -
83C LYS* 4.4 4.5 - - + -
84C LEU* 3.9 23.3 - - + -
278C SER* 4.4 17.4 - - - -
281C PRO* 4.4 8.7 - - + -
282C LEU* 3.9 27.1 - - + -
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Residues in contact with THR 6 (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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159B LEU 4.5 0.2 + - - -
161B ASP* 4.7 0.7 + - - -
163B ASN 5.4 0.3 - - - -
164B ILE* 3.3 29.9 - - + +
1C MET* 3.5 41.0 - - + +
3C PRO* 2.9 31.4 + - + +
5C PHE* 1.3 76.3 - - - +
7C GLN* 1.3 64.8 + - - +
9C ARG* 3.3 4.9 + - + +
10C ARG* 3.0 22.0 + - - +
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Residues in contact with GLN 7 (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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1C MET* 4.2 17.4 + - + +
2C GLN* 2.7 36.2 + - - +
3C PRO 3.1 7.2 + - - +
4C LEU* 3.2 30.2 + - + +
6C THR* 1.3 76.6 - - - +
8C GLU* 1.3 57.7 + - + +
10C ARG* 3.2 8.2 + - - +
11C ILE* 3.0 38.1 + - + +
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Residues in contact with GLU 8 (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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4C LEU* 2.8 25.7 + - + +
5C PHE* 3.7 11.0 - - + +
7C GLN* 1.3 74.7 - - + +
9C ARG* 1.3 66.1 + - - +
11C ILE* 3.2 22.3 + - - +
12C PHE* 2.9 24.1 + - - +
76C PHE* 3.7 22.1 - - + -
79C SER* 2.3 43.4 + - - -
80C ALA* 4.2 10.0 - - + -
83C LYS* 3.4 18.1 + - - +
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Residues in contact with ARG 9 (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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164B ILE* 3.6 22.9 - - + -
5C PHE 3.0 18.9 + - - +
6C THR* 3.5 7.6 - - - +
8C GLU* 1.3 76.4 - - - +
10C ARG* 1.3 63.0 + - - +
12C PHE* 3.3 6.8 + - + +
13C HIS* 3.1 43.7 + - + -
76C PHE* 3.8 10.9 - - + -
244C PHE 4.6 0.2 - - - -
245C ALA* 3.5 9.5 - - - +
246C LEU 3.6 1.2 - - - +
247C TYR* 3.5 20.6 - - - -
248C GLU* 2.8 41.4 + - - -
276C ASP* 2.9 38.2 + - - -
277C ILE* 4.0 14.4 - - + +
278C SER* 4.2 2.2 - - - -
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Residues in contact with ARG 10 (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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1C MET* 3.3 34.5 - - + +
6C THR 3.0 8.1 + - - +
7C GLN* 3.2 9.6 + - - +
9C ARG* 1.3 75.2 - - - +
11C ILE* 1.3 61.2 + - + +
13C HIS* 3.3 22.7 + - - +
14C LYS* 2.8 40.5 + - + +
17C LEU* 4.6 10.2 - - - +
51C LEU* 3.0 39.6 + - - +
52C HIS* 4.0 21.3 + - - +
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Residues in contact with ILE 11 (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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7C GLN* 3.0 24.1 + - + +
8C GLU* 3.6 26.0 - - - +
10C ARG* 1.3 74.6 - - + +
12C PHE* 1.3 63.8 + - - +
14C LYS* 3.2 9.6 + - + +
15C LYS* 2.9 50.0 + - + +
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Residues in contact with PHE 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLU 2.9 13.7 + - - +
9C ARG* 3.3 9.0 - - - +
11C ILE* 1.3 77.1 - - - +
13C HIS* 1.3 78.7 + + - +
15C LYS* 3.2 15.9 + - - +
16C LEU* 3.3 21.8 + - + +
69C PHE* 4.1 13.7 - + - -
72C ILE* 3.5 30.9 - - + +
73C CYS* 3.9 23.8 - - - -
76C PHE* 3.9 28.9 - + + -
244C PHE* 3.7 37.9 - - + -
277C ILE* 4.1 26.9 - - + -
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Residues in contact with HIS 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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9C ARG* 3.1 47.3 + - + +
10C ARG* 3.7 25.9 + - - +
12C PHE* 1.3 93.9 - + - +
14C LYS* 1.3 62.5 + - - +
16C LEU* 3.1 11.2 + - + +
17C LEU* 3.1 25.9 + - + +
22C LEU* 5.7 0.6 - - - +
51C LEU* 3.3 39.0 - - + +
244C PHE* 2.7 37.5 + + - -
245C ALA* 4.0 4.5 - - + +
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Residues in contact with LYS 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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10C ARG* 2.8 31.5 + - + +
11C ILE* 3.2 10.3 + - + +
13C HIS* 1.3 76.4 - - - +
15C LYS* 1.3 58.3 + - + +
17C LEU* 3.7 10.4 - - + +
18C ASP* 2.8 59.7 + - - +
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Residues in contact with LYS 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 2.9 40.3 + - + +
12C PHE* 3.5 9.0 - - - +
13C HIS 3.2 0.2 - - - -
14C LYS* 1.3 77.2 - - + +
16C LEU* 1.3 61.9 + - - +
18C ASP* 4.0 5.5 - - - +
19C GLY* 3.1 21.3 + - - -
72C ILE* 3.8 34.7 - - + +
75C GLU* 2.7 45.3 + - + +
76C PHE* 5.3 0.8 - - - +
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Residues in contact with LEU 16 (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 PHE* 3.3 30.0 + - + +
13C HIS* 3.1 13.7 + - + +
15C LYS* 1.3 80.0 - - - +
17C LEU* 1.3 56.9 + - - +
20C ASN 3.6 0.7 + - - -
21C ILE* 2.9 46.8 + - + -
22C LEU* 3.0 20.1 + - + -
69C PHE* 4.1 22.7 - - + -
72C ILE* 3.8 26.0 - - + -
188C TRP* 4.3 7.2 - - + -
244C PHE* 3.8 32.3 - - + -
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Residues in contact with LEU 17 (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 ARG* 4.6 11.4 - - - +
13C HIS* 3.1 14.4 + - + +
14C LYS* 3.7 11.9 - - + +
16C LEU* 1.3 77.8 - - - +
18C ASP* 1.3 64.7 + - - +
20C ASN* 2.9 27.9 + - - -
22C LEU* 3.5 38.4 - - + +
51C LEU* 3.7 26.2 - - + +
52C HIS 4.5 3.1 - - - +
53C SER* 3.6 32.3 - - - +
55C THR* 4.5 10.8 + - - +
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Residues in contact with ASP 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 LYS* 2.8 52.2 + - - +
15C LYS* 4.2 4.8 - - - +
17C LEU* 1.3 75.9 - - - +
19C GLY* 1.3 59.0 + - - +
20C ASN* 3.2 7.8 + - - -
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Residues in contact with GLY 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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15C LYS 3.1 15.9 + - - -
17C LEU 3.2 0.2 - - - -
18C ASP* 1.3 75.4 - - - +
20C ASN* 1.3 71.2 + - - +
21C ILE* 3.1 20.9 + - - +
60C LEU* 4.0 5.4 - - - +
72C ILE* 6.1 0.2 - - - -
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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