Contacts of the helix formed by residues 13 - 28 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE 3.3 0.2 - - - -
12B THR* 1.3 77.1 - - - +
14B HIS* 1.3 61.3 + - - +
15B ALA 3.4 2.0 - - - -
16B SER* 3.1 14.7 + - - -
17B ASP* 2.7 62.4 + - - +
1421C ALA 3.2 23.3 - - - +
1422C GLY* 3.2 24.3 - - - +
1423C ARG* 3.5 35.8 - - - +
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Residues in contact with HIS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.7 9.9 - - + -
53A CYS* 3.8 10.8 - - - -
89A PHE* 3.4 30.9 + + - -
90A MET 2.9 21.8 + - - -
93A SER* 3.2 39.7 - - - +
11B PHE* 3.3 21.5 + - + +
12B THR 3.5 0.2 - - - -
13B ARG* 1.3 78.3 - - - +
15B ALA* 1.3 56.6 + - - +
17B ASP* 3.1 2.3 + - - +
18B VAL* 2.8 48.1 + - + +
1424C SER* 2.6 30.5 + - - +
1425C ILE* 3.9 4.0 - - + -
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA* 3.6 32.5 - - + +
16A SER* 3.6 14.6 - - - +
19A LEU* 4.1 22.2 - - + +
93A SER* 3.5 6.6 + - - +
11B PHE 4.8 0.2 + - - -
12B THR 5.4 1.1 + - - +
13B ARG 3.4 0.6 - - - -
14B HIS* 1.3 77.9 - - - +
16B SER* 1.3 59.3 + - - +
18B VAL* 3.2 4.7 + - - +
19B LEU* 2.8 29.5 + - - +
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Residues in contact with SER 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA* 3.6 15.8 - - - +
13B ARG* 3.1 18.4 + - - -
15B ALA* 1.3 79.6 - - - +
17B ASP* 1.3 59.7 + - - +
19B LEU* 3.3 3.4 + - - +
20B LEU* 2.9 28.8 + - - +
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Residues in contact with ASP 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 2.7 61.3 + - - +
14B HIS 3.6 6.1 - - - +
16B SER* 1.3 72.9 + - - +
18B VAL* 1.3 66.0 + - - +
20B LEU* 3.4 6.6 + - - +
21B ASN* 3.1 27.5 + - - +
1423C ARG* 3.3 23.7 + - - +
1424C SER* 3.1 28.5 + - - +
1425C ILE* 3.8 13.5 - - + -
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.2 18.6 - - + -
22A LEU* 5.3 3.4 - - + -
49A VAL* 5.5 6.5 - - + -
52A ALA* 4.2 8.5 - - + +
53A CYS* 3.8 16.6 - - - -
90A MET 4.3 4.3 - - - +
14B HIS* 2.8 53.1 + - + +
15B ALA* 3.5 9.6 - - - +
17B ASP* 1.3 73.8 - - - +
19B LEU* 1.3 63.6 + - - +
21B ASN* 3.1 6.9 + - - +
22B LEU* 3.0 37.6 + - + +
1425C ILE* 3.8 7.0 - - + -
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A HIS* 3.8 13.9 - - + -
15A ALA* 4.1 12.3 - - + +
18A VAL* 4.2 23.1 - - + -
15B ALA 2.8 19.8 + - - +
16B SER* 3.7 4.3 - - - +
17B ASP 3.3 0.2 - - - -
18B VAL* 1.3 74.2 - - - +
20B LEU* 1.3 63.5 + - - +
22B LEU* 3.1 18.8 + - + +
23B ASN 3.0 16.1 + - - -
49B VAL* 5.4 2.7 - - + -
90B MET 3.8 13.9 - - - +
91B TYR* 3.3 34.2 - - + +
92B THR* 3.9 3.6 - - - +
93B SER* 3.6 24.9 - - - +
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B SER 2.9 16.9 + - - +
17B ASP* 3.8 5.8 - - - +
19B LEU* 1.3 76.1 - - - +
21B ASN* 1.3 60.2 + - - +
23B ASN* 3.0 17.2 + - + +
24B ARG* 2.9 66.0 + - + +
91B TYR 4.9 1.3 - - - -
1423C ARG* 4.0 22.4 - - - +
1427C GLU* 4.5 8.1 - - + +
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Residues in contact with ASN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA* 2.8 34.4 + - + -
17B ASP 3.1 14.1 + - - +
18B VAL 3.1 8.0 + - - +
20B LEU* 1.3 80.2 - - - +
22B LEU* 1.3 61.8 + - - +
24B ARG* 3.6 7.4 - - - +
25B LEU* 3.2 27.1 + - - +
1423C ARG* 4.7 2.0 + - - -
1425C ILE* 3.8 4.6 - - - +
1426C HIS* 2.8 23.0 + - - +
1427C GLU* 3.8 6.6 - - - +
1428C ILE* 3.1 44.7 + - + +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 5.2 2.0 - - + -
22A LEU* 4.4 17.5 - - + -
48A THR* 3.9 40.8 - - + +
49A VAL* 4.7 3.4 - - + +
52A ALA* 4.4 5.4 - - + -
18B VAL* 3.0 33.4 + - + +
19B LEU* 3.5 21.5 - - + +
20B LEU 3.1 0.4 - - - -
21B ASN* 1.3 76.7 - - - +
23B ASN* 1.3 62.7 + - - +
25B LEU* 3.4 10.6 + - + +
26B ARG* 3.1 20.6 + - - +
46B HIS* 3.7 4.3 - - + +
49B VAL* 4.3 19.7 - - + -
91B TYR* 3.6 16.9 - - + -
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Residues in contact with ASN 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU 3.0 5.1 + - - +
20B LEU* 3.0 19.4 + - + +
22B LEU* 1.3 77.2 - - - +
24B ARG* 1.3 65.4 + - - +
26B ARG* 2.6 46.5 + - - +
27B SER* 3.0 24.4 + - - -
88B ASP* 5.5 0.2 + - - -
91B TYR* 3.3 29.9 - - + +
92B THR* 3.8 18.8 - - - +
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Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 2.9 44.3 + - + +
21B ASN* 3.6 12.8 - - - +
22B LEU 3.2 0.2 - - - -
23B ASN* 1.3 77.4 - - - +
25B LEU* 1.3 63.1 + - - +
27B SER* 2.7 23.4 + - - -
28B ARG* 2.9 14.1 + - - +
1427C GLU* 3.0 27.9 + - - +
1428C ILE* 2.7 59.8 + - + +
1429C PRO* 4.2 2.4 - - - +
1430C ARG* 3.4 62.9 - - - +
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A THR* 4.2 41.7 - - + +
51A MET* 3.9 26.5 - - + -
52A ALA 5.3 0.4 - - - +
58A TYR* 4.4 2.9 - - + -
21B ASN 3.2 14.5 + - - +
22B LEU* 3.6 13.0 - - + +
23B ASN 3.3 0.2 - - - -
24B ARG* 1.3 76.1 - - - +
26B ARG* 1.3 58.4 + - - +
28B ARG* 3.1 2.2 + - - +
29B ASP 2.8 10.4 + - - -
30B ILE* 2.7 66.7 + - + +
46B HIS* 3.8 4.5 - - - +
1428C ILE* 4.0 20.0 - - + -
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Residues in contact with ARG 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU 3.1 10.4 + - - +
23B ASN* 2.6 41.0 + - - +
24B ARG 3.1 0.2 - - - -
25B LEU* 1.3 78.3 - - - +
27B SER* 1.3 59.4 + - - +
29B ASP* 2.9 21.7 + - - +
32B THR* 4.2 5.8 - - + +
44B ARG* 3.7 24.8 + - - +
45B ALA* 4.4 2.2 - - - -
46B HIS* 3.6 10.0 - - + +
84B ASN* 5.6 2.2 - - - +
87B LEU* 3.5 29.2 - - - +
88B ASP* 3.3 26.5 + - - +
91B TYR* 3.6 47.9 - - + +
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Residues in contact with SER 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASN* 3.0 14.6 + - - -
24B ARG* 2.7 25.6 + - - -
26B ARG* 1.3 76.5 - - - +
28B ARG* 1.3 63.0 + - - +
29B ASP* 3.1 3.6 + - - +
1430C ARG* 4.8 4.5 + - - +
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Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 3.3 27.0 + - - -
24B ARG 2.9 19.5 + - - +
27B SER* 1.3 78.8 + - - +
29B ASP* 1.3 70.5 + - - +
30B ILE* 3.0 30.5 + - + +
1428C ILE* 4.1 6.5 - - - +
1429C PRO* 3.1 45.7 + - - +
1430C ARG* 3.3 24.3 + - - +
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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
------------------------------------------------------------
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