Contacts of the helix formed by residues 3 - 19 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET 4.0 0.9 - - - +
2B GLN* 1.3 95.6 - - + +
4B LEU* 1.3 63.5 + - - +
6B THR* 3.1 19.7 + - - +
7B GLN* 3.0 18.9 + - - +
158C PHE* 3.5 23.7 - - + +
159C LEU 3.2 24.5 - - - +
160C VAL* 3.8 2.7 - - - -
161C ASP* 3.0 46.4 - - + +
164C ILE* 4.3 0.7 - - + -
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Residues in contact with LEU 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.8 14.8 - - + -
3B PRO* 1.3 73.7 - - - +
5B PHE* 1.3 60.0 + - - +
7B GLN* 3.3 30.9 + - + +
8B GLU* 2.8 32.2 + - - +
83B LYS* 4.0 21.3 - - + +
157C GLU* 3.6 41.3 - - + +
158C PHE 2.8 19.9 + - - +
159C LEU* 3.5 13.9 + - + -
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Residues in contact with PHE 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 1.3 77.4 - - - +
6B THR* 1.3 61.1 + - - +
8B GLU* 3.2 7.5 + - + +
9B ARG* 2.9 28.4 + - - +
76B PHE* 4.8 3.7 - + + -
80B ALA* 3.5 43.7 - - + -
83B LYS* 4.4 3.8 - - + -
84B LEU* 3.8 24.5 - - + -
278B SER* 4.7 10.0 - - - +
281B PRO* 4.4 8.1 - - + -
282B LEU* 4.0 26.7 - - + -
153C ILE* 5.4 0.2 - - + -
159C LEU* 3.0 36.2 + - + +
160C VAL* 3.5 23.6 - - + -
164C ILE* 4.0 16.8 - - + +
165C ALA* 4.7 6.5 - - + -
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Residues in contact with THR 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B GLN* 4.6 10.9 + - + +
3B PRO* 3.1 24.6 + - - +
5B PHE* 1.3 78.7 - - - +
7B GLN* 1.3 61.8 + - - +
9B ARG* 3.4 5.5 + - + +
10B ARG* 3.1 52.8 + - + +
161C ASP* 4.8 1.4 + - - -
163C ASN* 5.2 1.1 + - - +
164C ILE* 3.2 38.9 - - + +
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Residues in contact with GLN 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 4.1 12.1 - - - +
2B GLN* 2.8 35.6 + - + +
3B PRO 3.0 9.5 + - - +
4B LEU* 3.4 32.7 - - + +
5B PHE 3.2 0.2 - - - -
6B THR* 1.3 76.0 - - - +
8B GLU* 1.3 63.8 + - + +
10B ARG* 3.3 13.1 + - - +
11B ILE* 3.1 32.0 + - + +
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Residues in contact with GLU 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU 2.8 27.1 + - - +
5B PHE* 3.2 12.5 + - + +
7B GLN* 1.3 75.3 - - + +
9B ARG* 1.3 65.2 + - - +
11B ILE* 3.3 22.1 + - - +
12B PHE* 3.0 23.7 + - - +
76B PHE* 3.7 24.9 - - + +
79B SER* 2.6 36.1 + - - -
80B ALA* 4.3 14.1 + - + -
83B LYS* 3.7 17.0 - - - -
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Residues in contact with ARG 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE 2.9 15.9 + - - +
6B THR* 3.5 7.9 - - - +
7B GLN 3.3 0.2 - - - -
8B GLU* 1.3 76.3 - - - +
10B ARG* 1.3 65.1 + - + +
12B PHE* 3.2 6.0 - - - +
13B HIS* 3.1 42.1 + - + +
76B PHE* 3.9 10.3 - - + -
245B ALA* 3.4 9.5 - - - +
246B LEU 3.6 1.0 - - - +
247B TYR* 3.4 22.3 - - - -
248B GLU* 2.8 43.0 + - - -
276B ASP* 2.8 40.7 + - - -
277B ILE* 4.0 17.2 - - + +
278B SER* 4.2 2.7 - - - -
164C ILE* 3.7 19.3 - - + -
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Residues in contact with ARG 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B GLN* 3.9 28.8 + - - +
6B THR* 3.1 37.3 + - + +
7B GLN* 3.6 13.0 - - - +
8B GLU 3.2 0.2 - - - -
9B ARG* 1.3 76.4 - - + +
11B ILE* 1.3 59.1 + - + +
13B HIS* 3.3 10.2 + - - +
14B LYS* 2.8 38.7 + - + +
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Residues in contact with ILE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLN* 3.1 19.0 + - + +
8B GLU* 3.3 26.0 + - - +
10B ARG* 1.3 75.4 - - + +
12B PHE* 1.3 64.1 + - - +
14B LYS* 3.2 14.8 + - + +
15B LYS* 3.0 50.0 + - + +
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Residues in contact with PHE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLU 3.0 13.1 + - - +
9B ARG 3.2 10.3 - - - +
10B ARG 3.2 0.2 - - - -
11B ILE* 1.3 77.4 - - - +
13B HIS* 1.3 79.6 + + - +
15B LYS* 3.2 15.0 + - - +
16B LEU* 3.3 20.7 + - + +
69B PHE* 4.1 22.2 - + - -
72B ILE* 3.6 30.1 - - + +
73B CYS* 3.9 25.4 - - - -
76B PHE* 3.8 29.6 - + + -
219B VAL* 5.2 0.2 - - + -
244B PHE* 3.8 30.3 - - + -
277B ILE* 4.1 25.4 - - + -
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Residues in contact with HIS 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ARG* 3.1 44.2 + - + +
10B ARG* 3.6 11.9 - - - +
12B PHE* 1.3 97.0 - + - +
14B LYS* 1.3 62.0 + - - +
16B LEU* 3.0 18.1 + - + +
17B LEU* 3.0 20.5 + - + +
22B LEU* 5.8 0.3 - - - +
51B LEU* 3.4 46.7 - - + +
244B PHE* 2.7 34.6 + + - -
245B ALA* 3.9 4.7 - - + +
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Residues in contact with LYS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ARG* 2.8 31.0 + - + +
11B ILE* 3.2 13.0 + - + +
13B HIS* 1.3 73.1 - - + +
15B LYS* 1.3 57.5 + - + +
17B LEU* 3.8 10.9 - - + +
18B ASP* 2.8 55.5 + - - +
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Residues in contact with LYS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 3.0 38.1 + - + +
12B PHE* 3.6 8.1 - - - +
13B HIS 3.2 0.4 - - - -
14B LYS* 1.3 77.8 - - + +
16B LEU* 1.3 63.1 + - - +
18B ASP* 4.1 5.0 - - - +
19B GLY* 3.2 19.8 + - - -
72B ILE* 3.7 32.5 + - + +
75B GLU* 2.7 46.4 + - + +
76B PHE* 5.2 0.8 - - - +
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PHE* 3.3 30.9 + - + +
13B HIS* 3.0 13.1 + - + +
15B LYS* 1.3 78.9 - - - +
17B LEU* 1.3 59.0 + - + +
20B ASN 3.5 0.5 + - - -
21B ILE* 2.9 48.0 + - + +
22B LEU* 3.0 19.2 + - + -
69B PHE* 4.0 24.0 - - + -
72B ILE* 3.7 25.1 - - + -
188B TRP* 4.2 6.7 - - + -
244B PHE* 3.8 32.5 - - + -
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B HIS* 3.0 21.3 + - + +
14B LYS* 3.8 10.5 - - + +
15B LYS 3.3 0.2 - - - -
16B LEU* 1.3 72.8 - - - +
18B ASP* 1.3 68.8 + - - +
19B GLY 3.1 1.8 - - - -
20B ASN* 2.9 22.0 + - - -
22B LEU* 3.3 38.0 - - + +
51B LEU* 3.6 28.5 - - + +
52B HIS 4.8 1.8 - - - +
53B SER* 3.5 33.0 - - - +
55B THR* 4.8 6.9 + - - +
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Residues in contact with ASP 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LYS* 2.8 48.8 + - - +
15B LYS* 4.2 5.8 - - - +
17B LEU* 1.3 75.3 - - - +
19B GLY* 1.3 58.3 + - - +
20B ASN* 3.2 7.9 + - - +
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Residues in contact with GLY 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LYS 3.2 15.8 + - - -
17B LEU 3.1 0.6 - - - -
18B ASP* 1.3 76.2 - - - +
20B ASN* 1.3 68.8 + - - +
21B ILE* 3.0 23.1 + - - +
60B LEU* 3.7 5.7 - - - +
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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