Contacts of the helix formed by residues 9 - 26 (chain U) in PDB entry 2D2C
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 LEU 9 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5U GLY* 3.0 26.9 - - - +
6U TRP* 2.5 27.8 + - + +
7U VAL 2.4 13.6 + - - +
8U ALA* 1.3 79.4 - - + +
10U LEU* 1.3 57.3 + - - +
11U VAL 2.4 19.4 + - - -
12U VAL 2.8 13.0 + - - -
13U PHE* 3.1 39.3 + - + -
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Residues in contact with LEU 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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259P ILE* 6.1 4.9 - - + -
262P ILE* 5.5 4.9 - - + -
263P CYS* 4.6 19.1 - - - -
266P MET* 4.0 28.0 - - + -
8T LEU* 5.8 12.3 - - + -
11T ALA 4.3 17.5 - - - +
12T THR* 4.5 12.1 - - + +
15T GLY* 4.1 6.1 - - - +
6U TRP* 3.0 7.4 + - + +
7U VAL* 5.5 0.2 - - - -
9U LEU* 1.3 78.4 - - - +
11U VAL* 1.3 69.1 + - + +
13U PHE* 3.0 31.2 - - + +
14U THR* 3.2 16.4 + - - +
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Residues in contact with VAL 11 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266P MET* 5.4 1.1 - - - -
19S VAL* 5.7 3.1 - - + -
23S LEU* 4.6 20.2 - - + -
15T GLY* 3.3 29.6 - - - +
18T TYR* 4.9 10.2 - - + -
21T TYR* 5.0 13.7 - - + -
7U VAL* 2.9 47.6 - - + +
8U ALA* 5.8 0.2 - - - -
9U LEU 2.4 7.5 + - - -
10U LEU* 1.3 75.3 - - + +
12U VAL* 1.3 71.3 + - + +
14U THR* 3.0 15.7 + - - -
15U TRP* 3.2 8.2 + - + +
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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
----------------------------------------------------------
23S LEU* 6.3 2.7 - - + -
8U ALA* 2.9 31.2 - - - +
9U LEU 2.8 5.3 + - - -
11U VAL* 1.3 84.7 - - + +
13U PHE* 1.3 57.1 + - + +
15U TRP* 2.7 31.3 + - + +
16U SER* 2.5 40.7 + - - +
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Residues in contact with PHE 13 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8U ALA 4.4 3.4 - - - -
9U LEU* 3.1 56.3 - - + -
10U LEU* 3.0 27.5 + - + +
12U VAL* 1.3 82.7 - - + +
14U THR* 1.3 56.6 + - - +
16U SER* 3.7 13.1 + - - -
17U ILE* 3.1 23.2 - - - +
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Residues in contact with THR 14 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263P CYS* 6.1 0.3 - - - -
266P MET* 3.8 41.0 - - + +
267P LEU* 4.0 22.2 - - + -
270P LEU* 5.2 4.7 - - + +
18T TYR* 4.2 15.8 + - + +
10U LEU* 3.2 19.4 + - - +
11U VAL 3.0 7.3 + - - -
13U PHE* 1.3 73.4 - - - +
15U TRP* 1.3 66.0 + - - +
16U SER 3.1 1.6 - - - -
17U ILE* 3.0 24.3 + - + +
18U ALA* 3.1 12.0 + - - +
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Residues in contact with TRP 15 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23S LEU* 4.5 23.1 - - + +
26S LEU* 3.2 49.1 - - + -
27S LEU* 2.7 34.4 - - + +
30S ILE* 5.0 5.6 - - + -
18T TYR* 4.8 12.9 - + + -
11U VAL* 3.2 6.6 + - + +
12U VAL* 2.9 39.5 - - + +
14U THR* 1.3 78.3 - - - +
16U SER* 1.3 50.6 + - - +
17U ILE 2.7 1.9 + - - -
18U ALA* 2.7 38.4 + - + +
19U MET* 3.2 36.4 + - + +
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Residues in contact with SER 16 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U VAL* 2.5 23.9 + - - -
13U PHE* 3.7 14.8 - - - -
14U THR 3.1 0.4 - - - -
15U TRP* 1.3 71.2 - - - +
17U ILE* 1.3 60.4 + - - +
19U MET* 3.9 15.0 - - - +
20U VAL* 3.1 21.3 - - - +
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Residues in contact with ILE 17 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267P LEU* 5.1 11.4 - - + -
270P LEU* 5.5 2.9 - - + -
13U PHE 3.1 23.3 - - - +
14U THR* 3.4 21.1 - - + +
15U TRP 2.7 1.6 + - - -
16U SER* 1.3 79.4 - - - +
18U ALA* 1.3 62.7 - - - +
20U VAL* 3.4 7.2 - - - +
21U VAL* 3.0 44.9 + - + +
24U ARG* 5.3 8.7 - - - +
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Residues in contact with ALA 18 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270P LEU* 4.5 15.2 - - + +
274P LEU* 5.9 0.9 - - + -
27S LEU* 6.3 1.6 - - + -
18T TYR* 4.2 13.2 - - - +
14U THR 3.1 10.9 + - - +
15U TRP* 2.7 21.1 + - + +
17U ILE* 1.3 73.8 - - - +
19U MET* 1.3 63.6 + - - +
20U VAL 2.9 3.6 - - - -
21U VAL* 2.5 33.3 - - - +
22U TRP* 3.8 2.3 + - - +
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Residues in contact with MET 19 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30S ILE* 4.9 22.3 - - + +
15U TRP* 3.3 45.8 - - + +
16U SER* 3.9 12.8 - - - +
18U ALA* 1.3 75.8 - - + +
20U VAL* 1.3 91.8 + - - +
21U VAL 3.7 0.2 + - - -
22U TRP* 3.7 17.4 + - - +
23U GLY* 3.8 5.4 + - - -
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Residues in contact with VAL 20 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16U SER* 3.1 27.4 - - - +
17U ILE* 3.4 11.2 - - - +
18U ALA 2.9 0.4 + - - -
19U MET* 1.3 91.4 - - - +
21U VAL* 1.3 58.7 + - - +
23U GLY* 2.9 24.6 + - - -
24U ARG* 3.6 31.4 + - + +
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Residues in contact with VAL 21 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270P LEU* 5.5 3.6 - - + -
271P MET* 6.3 1.6 - - - -
274P LEU* 4.3 32.5 - - + -
22Q LEU* 6.3 3.8 - - + -
17U ILE* 3.0 25.2 + - + +
18U ALA* 2.5 37.4 + - - +
20U VAL* 1.3 68.7 - - - +
22U TRP* 1.3 65.7 + - - +
24U ARG* 3.0 39.6 + - - +
25U ASN* 2.8 20.0 - - - +
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Residues in contact with TRP 22 (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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30S ILE* 5.7 11.2 - - + -
31S GLN* 6.1 6.5 - - + -
18U ALA 3.8 1.1 + - - +
19U MET* 3.7 15.0 + - - +
20U VAL 3.3 0.6 - - - -
21U VAL* 1.3 81.4 - - - +
23U GLY* 1.3 80.1 + - - +
24U ARG 2.6 12.1 + - - -
25U ASN* 2.9 14.2 + - - +
26U GLY* 2.9 53.8 + - - -
27U LEU* 3.5 36.6 - - + -
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Residues in contact with GLY 23 (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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19U MET 3.8 0.8 + - - -
20U VAL 2.9 14.4 + - - -
22U TRP* 1.3 102.8 - - - +
24U ARG* 1.3 50.7 + - - +
27U LEU* 2.4 38.3 - - - +
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Residues in contact with ARG 24 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17U ILE* 5.3 7.7 - - - +
20U VAL* 4.0 29.8 - - + +
21U VAL* 3.2 36.3 - - - +
22U TRP 2.6 6.1 + - - -
23U GLY* 1.3 74.1 - - - +
25U ASN* 1.3 56.8 + - - +
27U LEU* 2.7 21.4 - - - +
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Residues in contact with ASN 25 (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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12Q ASP 6.0 0.3 + - - -
16Q ARG* 5.4 5.5 + - - -
19Q MET* 5.8 11.7 - - + +
21U VAL* 2.8 16.0 - - - +
22U TRP* 3.7 18.4 + - - +
24U ARG* 1.3 76.7 - - - +
26U GLY* 1.3 73.9 + - - +
27U LEU* 3.0 7.2 + - - +
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Residues in contact with GLY 26 (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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12Q ASP 5.5 8.7 + - - -
22U TRP* 2.9 39.2 + - - -
25U ASN* 1.3 80.0 - - - +
27U LEU* 1.3 65.6 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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