Contacts of the helix formed by residues 13 - 28 (chain A) in PDB entry 1R2B
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 ARG 13 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE 3.2 0.6 - - - -
12A THR* 1.3 77.7 + - - +
14A HIS* 1.3 53.9 + - - +
15A ALA 3.4 2.2 - - - -
16A SER* 3.1 14.6 + - - -
17A ASP* 2.7 66.8 + - - +
1421D ALA 3.1 24.4 + - - +
1422D GLY* 3.3 25.7 - - - +
1423D ARG* 3.6 36.2 - - - +
1424D SER* 4.7 0.4 - - - +
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Residues in contact with HIS 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 3.2 22.2 + - + +
13A ARG* 1.3 75.1 - - - +
15A ALA* 1.3 60.6 + - - +
17A ASP* 3.0 2.8 + - - +
18A VAL* 2.8 47.4 + - + +
19B LEU* 3.8 6.7 - - + -
53B CYS* 3.9 9.2 - - - -
89B PHE* 3.4 30.4 + + - -
90B MET 2.8 25.7 + - - -
93B SER* 3.1 40.2 - - - +
1424D SER* 2.7 32.0 + - - +
1425D ILE* 4.0 3.1 - - + -
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Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE 4.7 0.4 + - - -
12A THR 5.2 1.7 + - - +
13A ARG 3.4 0.6 - - - -
14A HIS* 1.3 78.8 - - - +
16A SER* 1.3 56.7 + - - +
18A VAL* 3.3 5.2 + - - +
19A LEU* 2.9 24.9 + - - +
15B ALA* 3.6 15.3 - - + +
16B SER* 3.6 37.7 - - - +
19B LEU* 4.1 22.6 - - + +
93B SER* 3.5 6.2 + - - +
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Residues in contact with SER 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR 5.6 0.2 + - - -
13A ARG* 3.1 19.1 + - - +
14A HIS 3.1 0.6 - - - -
15A ALA* 1.3 80.3 - - - +
17A ASP* 1.3 59.7 + - - +
19A LEU* 3.4 3.1 + - - +
20A LEU* 2.9 28.9 + - - +
15B ALA* 3.6 15.6 - - - +
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Residues in contact with ASP 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 2.7 62.2 + - - +
14A HIS 3.0 4.5 + - - +
16A SER* 1.3 72.8 + - - +
18A VAL* 1.3 64.7 + - - +
20A LEU* 3.5 6.2 + - - +
21A ASN* 3.1 28.6 + - - +
1423D ARG* 3.4 18.2 + - - +
1424D SER* 3.0 29.1 + - - +
1425D ILE* 3.7 20.9 - - + -
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A HIS* 2.8 49.5 + - + +
15A ALA* 3.6 7.2 - - - +
17A ASP* 1.3 74.9 - - - +
19A LEU* 1.3 66.2 + - - +
21A ASN* 3.1 4.2 + - - +
22A LEU* 2.9 39.8 + - + +
18B VAL* 6.6 0.2 - - + -
19B LEU* 4.2 17.5 - - + -
22B LEU* 5.2 3.4 - - + -
49B VAL* 5.4 6.7 - - + -
52B ALA* 4.2 9.8 - - + +
53B CYS* 3.8 12.3 - - - -
90B MET 4.3 2.9 - - - +
1425D ILE* 3.6 11.7 - - + -
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA 2.9 16.5 + - - +
16A SER* 3.8 4.3 - - - +
18A VAL* 1.3 77.2 - - - +
20A LEU* 1.3 64.3 + - - +
22A LEU* 3.2 16.4 + - + +
23A ASN* 3.0 22.3 + - - +
49A VAL* 5.3 3.4 - - + -
90A MET 3.6 15.7 - - - +
91A TYR* 3.3 27.7 - - + +
92A THR* 4.0 3.8 - - - +
93A SER* 3.7 23.1 - - - +
14B HIS* 3.7 16.6 - - + -
15B ALA* 4.1 13.2 - - + +
18B VAL* 4.2 22.9 - - + -
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Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A SER 2.9 16.9 + - - +
17A ASP* 3.8 5.8 - - - +
18A VAL 3.2 0.2 - - - -
19A LEU* 1.3 77.0 - - - +
21A ASN* 1.3 66.1 + - - +
23A ASN* 3.1 7.1 + - + +
24A ARG* 2.9 65.5 + - + +
91A TYR 5.1 1.1 - - - -
1423D ARG* 3.8 25.8 - - - +
1427D GLU* 4.5 6.1 - - + +
1430D ARG* 3.7 15.7 - - - +
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Residues in contact with ASN 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASP 3.1 20.1 + - - +
18A VAL 3.1 4.2 + - - +
20A LEU* 1.3 84.3 - - - +
22A LEU* 1.3 57.9 + - - +
24A ARG* 3.4 6.9 + - - +
25A LEU* 3.0 31.3 + - - +
52B ALA* 2.7 34.6 + - + -
1423D ARG* 4.7 1.3 + - - -
1425D ILE* 4.1 2.6 - - - +
1426D HIS 2.8 23.0 + - - +
1427D GLU* 3.9 3.6 - - - +
1428D ILE* 3.1 42.5 + - + +
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 2.9 34.9 + - + +
19A LEU* 3.6 20.2 - - + +
20A LEU 3.2 0.2 - - - -
21A ASN* 1.3 73.7 - - - +
23A ASN* 1.3 61.7 + - - +
25A LEU* 3.3 12.1 + - + +
26A ARG* 3.0 21.3 + - - +
46A HIS* 3.8 5.4 - - + +
49A VAL* 4.2 20.9 - - + -
91A TYR* 3.5 20.5 - - + -
18B VAL* 5.3 1.1 - - + -
22B LEU* 4.4 16.2 - - + -
48B THR* 3.8 42.6 - - + +
49B VAL* 4.7 2.9 - - + +
52B ALA* 4.4 3.6 - - + -
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Residues in contact with ASN 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU 3.0 11.9 + - - +
20A LEU* 3.4 11.8 - - + +
22A LEU* 1.3 75.3 - - - +
24A ARG* 1.3 66.8 + - - +
26A ARG* 2.9 44.8 + - - +
27A SER* 2.8 22.9 + - - -
91A TYR* 3.2 26.1 - - - +
92A THR* 3.7 17.1 - - - +
1430D ARG* 3.5 25.0 + - - +
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Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 2.9 43.5 + - + +
21A ASN* 3.4 10.3 - - - +
23A ASN* 1.3 76.3 - - - +
25A LEU* 1.3 62.8 + - - +
27A SER* 2.7 22.5 + - - -
28A ARG* 3.0 16.1 + - - +
1427D GLU* 2.5 38.6 + - - +
1428D ILE* 2.6 34.9 + - + +
1429D PRO* 4.1 10.3 - - - +
1430D ARG* 2.9 57.2 - - - +
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASN 3.0 20.3 + - - +
22A LEU* 3.4 20.6 - - + +
24A ARG* 1.3 77.1 - - - +
26A ARG* 1.3 56.6 + - - +
28A ARG* 3.5 2.5 + - - +
29A ASP 3.0 6.2 + - - -
30A ILE* 2.6 71.3 + - + +
46A HIS* 4.1 3.4 - - + -
48B THR* 4.0 32.8 - - + +
51B MET* 4.3 15.7 - - + -
52B ALA 4.9 0.7 - - - +
58B TYR* 4.1 13.2 - - + -
1428D ILE* 4.1 22.7 - - + -
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Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU 3.0 12.9 + - - +
23A ASN* 2.9 40.1 + - - +
25A LEU* 1.3 78.7 - - - +
27A SER* 1.3 59.1 + - - +
29A ASP* 2.9 20.4 + - - +
32A THR* 4.2 4.8 - - + +
44A ARG* 3.7 27.1 + - + +
45A ALA* 4.7 1.1 - - - -
46A HIS* 3.7 9.4 - - + -
84A ASN* 5.3 2.8 + - - -
87A LEU* 3.2 28.0 - - - +
88A ASP* 2.9 30.3 + - - +
91A TYR* 3.4 44.6 - - + +
92A THR* 5.3 0.2 - - - +
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Residues in contact with SER 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASN* 2.8 12.6 + - - -
24A ARG* 2.7 28.1 + - - -
26A ARG* 1.3 75.4 - - - +
28A ARG* 1.3 62.7 + - - +
29A ASP* 3.1 4.4 + - - +
1430D ARG* 3.6 24.7 + - - -
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Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG 3.0 18.4 + - - +
27A SER* 1.3 75.7 - - - +
29A ASP* 1.3 71.8 + - - +
30A ILE* 3.2 27.8 + - + +
58B TYR* 2.9 29.6 + - - -
1428D ILE* 3.6 13.1 - - - +
1429D PRO* 3.1 41.9 + - - +
1430D ARG* 3.5 22.3 + - - +
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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
------------------------------------------------------------
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