Contacts of the helix formed by residues 8 - 20 (chain U) in PDB entry 3IR0
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 GLY 8 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16S TYR* 3.1 35.5 - - - -
7T CYS* 4.9 1.6 - - - -
6U LEU 4.3 0.4 + - - -
7U CYS* 1.3 70.9 - - - +
9U SER* 1.3 63.1 + - - -
11U LEU* 3.2 21.5 + - - +
12U VAL* 3.6 6.2 + - - +
26U TYR* 4.8 5.0 + - - -
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Residues in contact with SER 9 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13S GLU* 3.3 30.0 + - - -
16S TYR* 3.7 23.3 - - - -
17S LEU* 6.2 0.4 - - - -
7U CYS 3.4 0.7 + - - -
8U GLY* 1.3 69.6 - - - -
10U HIS* 1.3 73.0 + - - +
11U LEU 3.2 0.2 - - - -
12U VAL* 3.6 10.9 - - - +
13U GLU* 3.1 28.3 + - - +
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Residues in contact with HIS 10 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6U LEU* 4.1 17.5 - - + +
7U CYS* 3.0 29.9 + - + +
9U SER* 1.3 83.4 + - - +
11U LEU* 1.3 62.8 + - - +
13U GLU* 3.7 7.4 + - - +
14U ALA* 3.2 22.5 + - - +
31U CU 2.0 32.1 - - - -
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Residues in contact with LEU 11 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2T ILE* 3.5 36.6 - - + +
3T VAL* 4.3 14.8 - - + +
6T CYS* 4.0 15.9 - - + -
7T CYS* 4.9 1.6 - - + -
16T LEU* 3.7 25.1 - - + -
6U LEU* 3.5 32.3 - - + +
7U CYS 3.8 1.2 + - - -
8U GLY 3.2 12.9 + - - +
9U SER 3.2 0.4 - - - -
10U HIS* 1.3 80.6 - - - +
12U VAL* 1.4 55.4 + - - +
14U ALA* 3.3 4.5 + - - +
15U LEU* 3.0 23.8 + - + +
26U TYR* 3.9 21.8 - - + +
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Residues in contact with VAL 12 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12S VAL* 3.5 23.6 - - + +
13S GLU* 5.1 2.5 - - - +
16S TYR* 3.9 19.1 - - + -
24S PHE* 4.0 9.0 - - + -
8U GLY 3.6 2.2 + - - +
9U SER* 3.6 24.0 - - - +
11U LEU* 1.4 72.3 - - - +
13U GLU* 1.3 61.9 + - - +
14U ALA 3.2 1.1 - - - -
15U LEU* 3.8 6.6 - - + +
16U TYR* 2.8 31.2 + - - +
24U PHE* 4.1 5.6 - - + -
26U TYR* 3.7 50.5 - - + -
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Residues in contact with GLU 13 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9S SER* 3.4 27.0 + - - +
10S HIS* 5.2 3.5 + - - -
12S VAL* 4.8 2.5 - - + -
13S GLU* 3.0 44.8 - - + +
9U SER 3.1 15.4 + - - +
10U HIS* 3.9 8.1 - - - +
12U VAL* 1.3 75.8 - - + +
14U ALA* 1.3 56.6 + - - +
16U TYR* 3.5 7.1 + - - +
17U LEU* 3.1 29.8 + - - +
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Residues in contact with ALA 14 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16T LEU* 4.1 20.6 - - + -
6U LEU* 4.2 17.5 - - + -
10U HIS 3.2 14.6 + - - +
11U LEU 3.3 10.1 - - - +
12U VAL 3.2 0.4 - - - -
13U GLU* 1.3 73.9 - - - +
15U LEU* 1.3 63.2 + - - +
17U LEU* 3.8 6.6 - - - +
18U VAL* 3.1 30.9 + - + +
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Residues in contact with LEU 15 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2T ILE* 3.7 22.9 - - + -
16T LEU* 3.4 46.0 - - + +
19T TYR* 3.9 19.3 - - + +
20T CYS* 4.9 3.1 - - - -
11U LEU 3.0 19.7 + - - +
12U VAL* 3.4 14.3 + - + +
14U ALA* 1.3 72.4 - - - +
16U TYR* 1.3 71.4 + - - +
18U VAL* 3.2 4.6 + - - -
19U CYS* 3.1 24.4 + - - -
24U PHE* 3.8 34.1 - - + -
25U PHE 4.1 5.8 - - - +
26U TYR* 4.6 1.8 - - + -
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Residues in contact with TYR 16 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8S GLY* 3.2 27.2 - - - -
9S SER* 3.3 33.2 + - - -
12S VAL* 4.0 15.3 - - + -
26S TYR* 3.8 33.4 - + - -
12U VAL 2.8 23.1 + - - +
13U GLU* 3.8 4.9 - - - +
15U LEU* 1.3 74.0 - - - +
17U LEU* 1.3 78.4 + - + +
20U GLY* 2.7 43.3 + - - -
24U PHE* 3.7 16.3 - - + -
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Residues in contact with LEU 17 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T LEU* 5.7 4.0 - - + -
13U GLU 3.1 15.9 + - - +
14U ALA* 3.8 6.5 - - - +
16U TYR* 1.3 92.4 - - + +
18U VAL* 1.3 70.9 + - + +
19U CYS 3.6 0.5 + - - -
20U GLY* 4.5 2.7 + - - -
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Residues in contact with VAL 18 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T LEU* 3.7 41.1 - - + +
16T LEU* 4.6 9.9 - - + -
17T GLU* 3.6 42.1 - - + +
20T CYS* 4.1 7.9 - - - -
14U ALA* 3.1 19.3 + - + +
15U LEU* 3.2 6.4 + - - +
16U TYR 3.0 1.4 + - - -
17U LEU* 1.3 86.6 - - + +
19U CYS* 1.3 56.8 + - - +
22U ARG* 4.4 2.3 + - - -
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Residues in contact with CYS 19 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20T CYS* 2.1 49.8 - - + -
15U LEU* 3.1 17.7 - - - -
16U TYR 2.9 2.4 + - - -
17U LEU 4.8 1.1 - - - -
18U VAL* 1.3 78.6 - - - +
20U GLY* 1.3 65.0 + - - +
21U GLU* 3.1 7.1 + - - +
22U ARG* 3.6 26.5 + - - +
23U GLY 2.9 26.0 - - - +
24U PHE* 3.6 11.9 - - + -
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Residues in contact with GLY 20 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26S TYR* 3.8 21.1 - - - -
28S PRO* 4.2 1.4 - - - +
16U TYR* 2.7 36.8 + - - +
17U LEU* 4.5 1.9 + - - -
19U CYS* 1.3 69.7 - - - +
21U GLU* 1.3 65.3 + - - -
22U ARG 3.3 1.0 + - - -
23U GLY* 3.3 10.2 + - - -
24U PHE* 5.8 0.6 - - - -
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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