Contacts of the helix formed by residues 3 - 23 (chain A) in PDB entry 2R5N
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 SER 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A SER* 1.3 77.2 - - - +
4A ARG* 1.3 64.5 + - - +
5A LYS* 3.5 9.1 + - - +
6A GLU* 3.0 37.5 + - - +
7A LEU* 3.0 21.5 + - - +
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Residues in contact with ARG 4 (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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2A SER 4.0 0.2 + - - -
3A SER* 1.3 72.8 - - - +
5A LYS* 1.3 58.9 + - + +
7A LEU* 3.2 7.3 + - + +
8A ALA* 2.9 28.9 + - - +
38A GLU* 2.8 52.2 + - - +
39A VAL* 3.7 17.7 - - - +
42A ARG* 4.0 9.3 - - - +
43A ASP* 2.9 44.2 + - - -
221A ALA* 3.6 27.1 + - + +
225A LYS* 4.5 10.3 - - - +
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Residues in contact with LYS 5 (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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3A SER* 3.2 9.0 + - - +
4A ARG* 1.3 78.9 - - + +
6A GLU* 1.3 57.1 + - + +
8A ALA* 3.2 6.5 + - - +
9A ASN* 2.8 43.2 + - - +
12A ARG* 5.9 0.4 - - - +
35A ASP* 4.5 10.7 - - - +
219A HIS* 2.7 30.1 + - - +
220A ASP* 4.5 8.9 + - - +
221A ALA* 5.2 2.7 - - + +
249A PHE* 5.9 8.0 - - + -
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Residues in contact with GLU 6 (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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2A SER* 3.5 18.1 - - - -
3A SER* 3.0 39.3 + - - +
5A LYS* 1.3 77.3 - - + +
7A LEU* 1.3 65.1 - - - +
9A ASN* 3.1 20.6 + - - +
10A ALA 3.3 8.8 + - - -
277A LEU 6.0 0.7 - - - +
279A TRP* 3.5 10.3 - - - -
290A ILE* 4.9 2.0 - - + +
677A EDO 2.7 39.2 + - - +
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Residues in contact with LEU 7 (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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2A SER* 3.8 21.8 - - - +
3A SER 3.0 14.8 + - - +
4A ARG* 3.2 9.2 + - + +
6A GLU* 1.3 75.2 - - - +
8A ALA* 1.3 63.1 + - - +
10A ALA* 3.3 12.2 + - - +
11A ILE 4.0 0.2 + - - -
38A GLU* 4.0 9.9 - - + +
42A ARG* 3.3 39.3 - - - +
290A ILE* 4.2 12.1 - - + -
293A GLN* 3.9 31.6 - - + +
294A TRP* 2.9 43.8 + - + +
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Residues in contact with ALA 8 (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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4A ARG 2.9 16.5 + - - +
5A LYS 3.6 2.5 - - - +
7A LEU* 1.3 74.6 - - - +
9A ASN* 1.3 58.5 + - - +
11A ILE* 3.0 31.1 + - - +
12A ARG* 3.3 5.1 + - - +
34A ALA* 3.5 26.4 - - - +
35A ASP* 3.2 30.5 - - - +
38A GLU* 4.0 11.3 - - + +
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Residues in contact with ASN 9 (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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5A LYS* 2.8 33.7 + - - +
6A GLU* 3.1 13.3 + - - +
8A ALA* 1.3 70.4 - - - +
10A ALA* 1.3 59.2 + - - +
12A ARG* 2.9 36.1 + - - +
13A ALA* 2.8 31.4 + - - +
249A PHE* 5.1 0.3 - - - -
277A LEU* 3.3 48.3 + - + +
279A TRP* 3.8 16.9 - - + -
677A EDO 5.4 0.6 + - - -
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Residues in contact with ALA 10 (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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6A GLU 3.3 5.0 + - - +
7A LEU 3.3 14.6 + - - +
8A ALA 3.1 0.2 - - - -
9A ASN* 1.3 77.8 - - - +
11A ILE* 1.3 61.3 + - - +
13A ALA* 3.5 1.0 + - - +
14A LEU* 3.0 31.4 + - - +
77A LEU* 4.1 10.3 - - + -
279A TRP* 3.5 28.4 - - + -
286A ILE* 4.3 7.1 - - + +
290A ILE* 4.3 12.1 - - + -
294A TRP* 4.1 11.7 - - - +
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Residues in contact with ILE 11 (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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8A ALA* 3.0 9.3 + - - +
10A ALA* 1.3 75.3 - - - +
12A ARG* 1.3 64.9 + - - +
15A SER* 2.8 41.8 + - - +
30A PRO 4.2 4.5 - - - +
34A ALA* 3.8 29.8 - - + +
37A ALA* 4.1 6.5 - - + -
70A LEU* 3.6 23.6 - - + -
73A SER* 3.7 18.7 + - - -
74A LEU* 3.8 20.4 - - + -
77A LEU* 4.1 17.0 - - + -
294A TRP* 3.8 23.1 - - + -
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Residues in contact with ARG 12 (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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5A LYS* 4.6 1.0 + - - +
8A ALA* 3.3 9.6 + - - +
9A ASN* 2.9 33.5 + - - +
11A ILE* 1.3 77.9 - - - +
13A ALA* 1.3 56.5 + - - +
15A SER* 3.8 2.0 - - - -
16A MET* 2.9 36.4 + - - +
31A MET* 2.8 47.4 + - + +
34A ALA* 3.6 18.8 - - + +
35A ASP* 2.7 44.9 + - - +
219A HIS* 3.7 6.5 + - - -
249A PHE* 3.5 39.2 + - - -
277A LEU* 3.9 21.3 - - + -
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Residues in contact with ALA 13 (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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9A ASN 2.8 17.8 + - - +
10A ALA 3.9 3.4 - - - +
12A ARG* 1.3 71.4 - - - +
14A LEU* 1.3 66.9 + - + +
16A MET* 3.6 13.4 - - + +
17A ASP* 2.9 39.4 + - - +
274A ARG* 4.5 0.9 - - - +
277A LEU* 5.5 0.6 - - + +
279A TRP* 3.3 42.0 - - + +
286A ILE* 5.8 0.7 - - + -
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Residues in contact with LEU 14 (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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10A ALA 3.0 20.5 + - - +
13A ALA* 1.3 76.7 - - + +
15A SER* 1.3 57.9 + - - +
17A ASP* 4.7 2.9 - - - -
18A ALA* 2.9 34.7 + - - +
69A MET* 3.9 1.8 - - - -
73A SER* 3.5 21.3 - - - +
76A HIS* 4.4 5.8 - - + -
77A LEU* 4.1 30.7 - - + -
84A MET* 3.8 33.0 - - + -
87A LEU* 4.1 19.5 - - + -
284A PHE* 4.2 19.2 - - + +
286A ILE* 4.1 15.0 - - + -
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Residues in contact with SER 15 (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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11A ILE* 2.8 25.7 + - - +
12A ARG* 3.8 3.8 - - - -
14A LEU* 1.3 74.3 - - - +
16A MET* 1.3 66.9 + - - +
18A ALA* 3.9 0.7 - - - +
19A VAL* 3.0 31.5 + - - +
27A PRO* 5.2 2.7 - - - -
30A PRO* 3.5 25.1 - - - +
31A MET* 5.2 3.4 - - - -
69A MET* 3.5 28.8 + - - +
73A SER* 3.4 11.3 + - - -
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Residues in contact with MET 16 (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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12A ARG 2.9 21.7 + - - +
13A ALA* 3.6 18.8 - - + +
15A SER* 1.3 73.6 - - - +
17A ASP* 1.3 65.3 + - - +
19A VAL* 3.5 2.1 + - - +
20A GLN* 2.9 29.5 + - - +
27A PRO* 4.5 10.5 - - - +
31A MET* 4.1 12.8 - - - +
265A LEU* 4.0 24.5 + - + -
270A ILE* 3.6 19.8 - - + +
273A THR* 3.6 35.7 - - + -
274A ARG* 3.9 36.3 - - + +
277A LEU* 4.8 4.7 - - + -
279A TRP* 5.6 1.1 - - + -
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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
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13A ALA* 2.9 25.5 + - - +
14A LEU* 4.1 3.1 - - - +
16A MET* 1.3 76.6 - - - +
18A ALA* 1.3 59.7 + - - +
20A GLN* 3.3 5.8 + - - +
21A LYS* 3.0 29.6 + - - +
270A ILE* 3.7 12.5 - - - +
274A ARG* 2.6 47.7 + - - -
283A PRO* 3.3 29.6 - - + +
284A PHE* 3.8 13.1 + - + +
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Residues in contact with ALA 18 (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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14A LEU 2.9 21.6 + - - +
17A ASP* 1.3 72.7 - - - +
19A VAL* 1.3 66.4 + - - +
21A LYS* 3.4 2.3 + - - +
22A ALA* 3.1 24.1 + - - +
69A MET* 3.4 31.9 - - + -
87A LEU* 3.8 15.9 - - + +
90A PHE* 3.7 7.5 - - + +
284A PHE* 3.9 14.8 - - + -
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Residues in contact with VAL 19 (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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15A SER 3.0 18.8 + - - +
16A MET* 3.8 5.6 - - - +
18A ALA* 1.3 76.3 - - - +
20A GLN* 1.3 62.3 + - - +
22A ALA 3.3 0.7 + - - -
23A LYS* 2.9 18.7 + - - -
24A SER 3.3 23.3 + - - +
25A GLY 3.7 17.3 - - - +
26A HIS 3.9 27.1 - - - +
27A PRO* 4.2 8.1 - - + -
69A MET* 4.2 7.9 - - + -
90A PHE* 3.9 15.3 - - + -
264A PRO* 3.7 22.8 - - + +
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Residues in contact with GLN 20 (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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16A MET 2.9 18.6 + - - +
17A ASP* 3.6 6.1 - - - +
18A ALA 3.2 0.2 - - - -
19A VAL* 1.3 77.2 - - - +
21A LYS* 1.3 62.6 + - - +
23A LYS* 3.0 27.1 + - - +
264A PRO* 3.3 19.7 - - - +
265A LEU 3.5 2.1 + - - -
266A GLY* 2.9 40.8 + - - +
267A ASP* 3.4 30.3 + - - +
270A ILE* 3.4 19.7 - - + +
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Residues in contact with LYS 21 (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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17A ASP 3.0 16.3 + - - +
18A ALA 3.9 4.0 - - - +
19A VAL 3.3 0.2 - - - -
20A GLN* 1.3 77.5 - - - +
22A ALA* 1.3 60.0 + - - +
23A LYS* 3.4 8.0 + - - +
87A LEU 6.0 0.2 - - - +
88A LYS* 2.8 44.6 + - - +
89A ASN* 4.5 4.2 + - - -
92A GLN* 6.2 0.8 - - - +
284A PHE* 3.7 28.5 - - + -
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Residues in contact with ALA 22 (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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18A ALA 3.1 16.4 + - - +
21A LYS* 1.3 75.4 - - - +
23A LYS* 1.3 68.8 + - - +
24A SER* 3.1 23.5 + - - +
90A PHE* 3.4 31.0 - - + +
91A ARG* 4.1 7.2 - - + -
92A GLN* 4.2 12.6 + - - +
468B GLU* 4.3 7.6 - - - +
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Residues in contact with LYS 23 (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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19A VAL 2.9 6.6 + - - -
20A GLN* 3.0 21.6 + - - +
21A LYS 4.1 6.3 - - - +
22A ALA* 1.3 80.6 - - - +
24A SER* 1.3 58.2 + - - +
264A PRO* 3.5 18.6 - - + +
468B GLU* 5.4 0.5 - - - +
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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
------------------------------------------------------------
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