Contacts of the helix formed by residues 12 - 25 (chain L) in PDB entry 2FIE
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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ASN* 4.7 3.6 + - - -
39A THR* 5.0 10.3 + - + +
84A MET* 5.1 9.4 - - + -
59H ILE* 6.3 2.5 - - + -
10L VAL* 5.4 4.0 - - + -
11L ASN* 1.3 83.6 + - - +
13L LEU* 1.3 67.2 + - - +
14L THR* 3.7 4.5 + - - -
15L ARG* 3.2 26.6 + - + +
16L PHE* 2.8 23.9 + - - +
184L PHE* 4.0 4.9 - - - -
192L GLU* 3.8 33.9 + - + -
193L PHE 3.1 11.7 - - - +
194L ILE* 4.5 5.6 - - + +
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Residues in contact with LEU 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L THR* 1.3 71.5 - - - +
14L THR* 1.3 66.2 + - - +
16L PHE* 3.0 4.4 + - + +
17L VAL* 2.9 29.2 + - + +
34L LEU* 5.2 4.9 - - + +
38L CYS* 3.4 35.9 - - + -
173L LEU* 3.5 27.4 - - + -
175L LEU* 4.2 19.5 - - + -
184L PHE* 3.6 36.8 - - + -
192L GLU* 5.0 1.1 + - - +
193L PHE* 2.7 29.8 + - + +
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Residues in contact with THR 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A THR* 4.4 1.5 + - + -
18A MET* 4.4 9.8 - - + +
35A ASN* 3.5 37.2 + - - +
12L THR* 3.3 5.7 + - - -
13L LEU* 1.3 81.1 - - - +
15L ARG* 1.3 59.2 + - - +
17L VAL* 3.2 6.2 + - - +
18L MET* 2.8 53.4 + - + +
35L ASN* 3.7 18.8 + - - +
38L CYS* 5.1 5.5 - - - -
192L GLU* 4.2 10.6 + - - -
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Residues in contact with ARG 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLN* 3.9 12.1 - - + +
35A ASN* 4.6 4.9 + - - +
36A SER* 3.6 19.4 + - - -
84A MET* 3.6 29.1 + - - +
87A SER* 2.8 48.1 + - - -
88A SER* 3.4 4.7 - - - +
10L VAL* 2.7 32.3 + - - +
11L ASN* 2.9 27.8 + - - +
12L THR* 3.2 16.8 + - - +
14L THR* 1.3 80.9 - - - +
16L PHE* 1.3 61.8 + - - +
18L MET* 3.3 8.8 + - - +
19L GLU* 3.0 51.3 + - - +
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Residues in contact with PHE 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L ASN* 3.2 11.1 + - + +
12L THR 2.8 19.8 + - - +
13L LEU 3.0 5.4 + - - +
15L ARG* 1.3 79.9 - - - +
17L VAL* 1.3 75.3 + - + +
19L GLU* 3.2 4.7 + - - +
20L GLU* 3.1 43.4 + - + +
175L LEU* 4.2 17.7 - - + -
177L MET* 4.8 7.6 - - - -
179L CYS* 4.5 9.9 - - - -
182L ASN* 3.1 37.0 - - - -
184L PHE* 3.8 23.1 - + + -
195L LEU* 4.6 12.8 - - + -
198L LYS* 5.9 6.1 - - - -
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Residues in contact with VAL 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A MET* 6.0 0.7 - - + -
13L LEU* 2.9 21.2 + - + +
14L THR* 3.7 8.3 - - - +
16L PHE* 1.3 88.5 - - + +
18L MET* 1.3 59.4 + - + +
20L GLU* 3.3 1.6 + - - -
21L GLY* 2.9 25.5 + - - -
31L THR* 3.4 38.5 + - + +
34L LEU* 3.6 29.8 - - + -
35L ASN 5.9 0.2 - - - +
175L LEU* 4.3 9.9 - - + -
1001L A74 3.5 19.2 - - + +
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Residues in contact with MET 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A THR* 4.9 3.1 - - + -
18A MET* 3.1 38.4 - - + -
31A THR* 3.4 33.2 - - + +
32A GLN* 3.9 33.0 - - + +
35A ASN* 4.7 5.4 - - + +
701A A74 4.7 1.6 - - - -
14L THR* 2.8 36.3 + - + +
15L ARG* 3.7 6.5 - - - +
17L VAL* 1.3 77.4 - - - +
19L GLU* 1.3 58.2 + - - +
21L GLY* 3.3 1.2 + - - -
22L ARG* 3.1 32.1 + - - +
31L THR* 4.6 4.0 - - + -
1001L A74 3.7 19.5 - - - +
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Residues in contact with GLU 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLN* 3.2 24.8 + - - +
87A SER 4.8 0.2 - - - +
88A SER 4.7 0.5 - - - +
89A PHE* 4.6 19.2 - - - -
11L ASN* 4.3 11.1 + - - -
15L ARG* 3.0 33.3 + - - +
16L PHE* 3.8 4.7 - - - +
18L MET* 1.3 73.0 - - - +
20L GLU* 1.3 70.3 + - - +
22L ARG* 3.1 10.0 + - - +
23L LYS* 2.9 39.5 + - - +
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Residues in contact with GLU 20 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16L PHE* 3.1 38.9 + - + +
17L VAL 3.6 7.2 - - - +
19L GLU* 1.3 77.4 - - - +
21L GLY* 1.3 63.5 + - - +
23L LYS* 3.2 34.5 + - - +
24L ALA* 3.1 19.8 + - - +
177L MET* 5.7 2.0 - - + -
179L CYS* 3.8 27.7 - - - +
1001L A74 3.8 28.7 - - + -
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Residues in contact with GLY 21 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17L VAL 2.9 15.1 + - - -
18L MET 3.6 0.4 - - - -
19L GLU 3.1 0.2 - - - -
20L GLU* 1.3 78.6 - - - +
22L ARG* 1.3 60.0 + - - +
24L ALA* 3.6 0.9 + - - -
25L ARG 3.1 14.0 + - - -
26L GLY 3.6 0.7 + - - -
1001L A74 2.9 58.0 + - - +
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Residues in contact with ARG 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A THR* 3.4 22.4 + - - +
29A GLU* 3.3 41.0 - - - +
32A GLN* 2.5 35.5 + - - -
89A PHE* 4.7 10.1 + - - +
90A ALA* 5.7 0.2 - - - +
18L MET 3.1 12.3 + - - +
19L GLU* 3.1 8.9 + - - +
21L GLY* 1.3 73.4 - - - +
23L LYS* 1.3 69.2 + - - +
25L ARG* 3.0 20.3 + - - +
1001L A74 3.3 46.1 - - + -
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Residues in contact with LYS 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L GLU* 2.9 27.2 + - - +
20L GLU* 3.2 35.6 + - - +
22L ARG* 1.3 80.4 - - - +
24L ALA* 1.3 61.6 + - + +
25L ARG* 3.2 14.6 + - - +
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Residues in contact with ALA 24 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20L GLU 3.1 4.1 + - - +
23L LYS* 1.3 78.5 - - + +
25L ARG* 1.3 76.2 + - - +
26L GLY* 3.1 2.4 + - - -
1001L A74 3.1 38.8 - - + +
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Residues in contact with ARG 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701A A74 6.1 0.2 - - - +
21L GLY 3.1 2.8 + - - -
22L ARG 3.0 20.4 + - - +
23L LYS 3.7 12.3 + - - +
24L ALA* 1.3 79.9 + - - +
26L GLY* 1.3 65.8 + - - +
1001L A74 3.5 40.5 - - + +
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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