Contacts of the helix formed by residues 11 - 24 (chain B) in PDB entry 2D2I
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 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B GLY 3.0 8.5 + - - -
10B PHE* 1.3 74.4 - - - +
12B ARG* 1.3 58.2 + - - -
13B ILE 3.4 1.8 - - - -
14B GLY* 3.7 0.9 - - - -
15B ARG* 2.7 50.1 + - - +
2341B NAP 2.9 32.7 + - - -
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Residues in contact with ARG 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLY* 1.3 70.5 - - - +
13B ILE* 1.3 61.9 + - + +
15B ARG* 3.0 28.2 - - - +
16B ASN* 2.8 46.2 + - - +
50B ASP* 2.7 45.1 + - - +
51B SER* 5.1 2.4 - - - +
52B VAL* 4.0 10.6 - - - +
53B LEU* 4.8 1.2 - - - +
186B LEU* 3.8 19.7 - - + -
319B GLU* 2.8 46.7 + - + +
2341B NAP 2.9 35.6 + - - +
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Residues in contact with ILE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ARG* 1.3 74.6 - - + +
14B GLY* 1.3 58.7 + - - +
17B PHE* 2.7 36.2 + - + +
96B ILE* 5.9 0.2 - - + -
98B SER* 4.3 5.8 - - - -
122B THR* 3.7 33.2 - - + +
319B GLU* 4.3 13.5 - - + -
322B TYR* 4.3 8.3 - - + -
323B SER* 3.9 18.8 - - - +
326B VAL* 4.9 3.1 - - + -
2341B NAP 3.0 75.0 + - + +
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Residues in contact with GLY 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ILE* 4.2 12.3 - - - +
9B GLY 3.6 20.4 + - - -
10B PHE* 4.1 7.9 - - - -
11B GLY* 3.2 7.9 + - - -
13B ILE* 1.3 81.9 - - - +
15B ARG* 1.3 62.0 + - - +
17B PHE* 3.5 5.5 + - - +
18B LEU* 3.1 19.4 + - - +
96B ILE* 6.1 0.7 - - - -
98B SER* 3.7 12.1 + - - -
2341B NAP 4.7 0.2 + - - -
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Residues in contact with ARG 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PHE* 2.9 62.9 + - + +
11B GLY* 2.7 37.7 + - - +
12B ARG* 3.0 39.6 - - - +
14B GLY* 1.3 69.9 - - - -
16B ASN* 1.3 65.9 + - - +
18B LEU* 3.3 3.3 + - - +
19B ARG* 3.0 31.3 + - - +
46B LEU* 3.2 59.2 + - - +
47B LEU* 4.1 7.7 - - + +
49B TYR 5.8 0.4 + - - -
50B ASP* 5.0 3.9 + - - +
53B LEU* 5.8 0.4 - - - -
2341B NAP 5.0 0.4 + - - -
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Residues in contact with ASN 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ARG* 2.8 40.8 + - - +
13B ILE* 3.6 1.3 - - - +
15B ARG* 1.3 74.9 - - - +
17B PHE* 1.3 61.6 + - - +
19B ARG* 3.2 2.4 + - - +
20B CYS* 2.8 33.6 + - - +
50B ASP* 4.8 0.6 + - - -
53B LEU* 3.4 27.0 - - - +
319B GLU* 3.7 30.1 + - - +
320B TRP* 3.5 27.2 + - - +
323B SER* 3.1 21.3 - - - +
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Residues in contact with PHE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B VAL* 4.8 3.4 - - + -
7B ILE* 3.9 27.6 - - + -
13B ILE* 2.7 23.7 + - + +
14B GLY* 3.6 4.7 - - - +
16B ASN* 1.3 71.7 - - - +
18B LEU* 1.3 67.9 + - - +
20B CYS* 3.1 4.7 + - - +
21B TRP* 2.9 26.0 + - + +
29B LEU* 4.2 19.5 - - + -
31B VAL* 4.3 15.3 - - + -
96B ILE* 4.0 31.4 - - + -
323B SER* 3.7 10.2 + - - +
326B VAL* 3.2 36.3 - - + -
327B VAL* 3.4 32.3 - - + +
330B ALA* 4.5 1.3 - - + -
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ILE* 3.8 21.3 - - + -
10B PHE* 3.8 24.9 - - + -
14B GLY 3.1 9.4 + - - +
15B ARG* 3.6 8.1 - - - +
16B ASN 3.3 0.2 - - - -
17B PHE* 1.3 83.5 - - - +
19B ARG* 1.3 61.9 + - - +
21B TRP* 3.3 16.2 + - + +
22B PHE* 3.0 62.3 + - + -
31B VAL* 4.3 5.2 - - + -
34B ILE* 4.3 3.4 - - + -
47B LEU* 4.0 22.0 - - + -
74B MET* 4.1 21.5 - - + -
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Residues in contact with ARG 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ARG* 3.0 20.3 + - - +
16B ASN* 3.2 3.6 + - - +
18B LEU* 1.3 72.0 - - - +
20B CYS* 1.3 68.1 + - - +
22B PHE* 3.3 3.5 + - - +
23B GLY* 3.1 18.5 + - - -
47B LEU* 3.3 29.2 + - + +
48B GLU 3.9 0.6 + - - -
50B ASP* 3.6 17.1 + - - +
53B LEU* 3.7 33.7 + - - +
54B GLY 3.0 28.9 + - - -
55B ARG 3.5 5.1 + - - -
56B PHE* 3.4 63.3 - - + +
320B TRP* 4.0 18.4 - - + -
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Residues in contact with CYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ASN 2.8 19.8 + - - +
17B PHE* 3.4 4.9 - - - +
19B ARG* 1.3 77.2 - - - +
21B TRP* 1.3 63.6 + - - +
23B GLY* 3.0 12.1 + - - -
24B ARG* 3.2 15.5 + - - -
320B TRP* 3.7 33.2 - - - -
323B SER* 3.9 3.8 - - - -
324B GLN* 3.1 54.7 + - - +
327B VAL* 3.9 9.9 - - + -
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Residues in contact with TRP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE* 2.9 19.1 + + + +
18B LEU* 3.4 11.4 - - + +
20B CYS* 1.3 75.4 - - - +
22B PHE* 1.3 95.1 + + - +
24B ARG* 2.7 36.4 + - + +
27B THR* 2.9 34.2 + - + -
29B LEU* 3.0 41.7 - - + +
30B GLU* 3.9 2.5 - - + -
31B VAL* 3.4 48.7 - - + -
72B LYS* 3.7 32.8 - - + -
74B MET* 5.0 0.9 - - - -
327B VAL* 4.0 14.5 - - + +
331B GLU* 4.3 2.9 - - - -
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Residues in contact with PHE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 3.0 50.0 + - + +
19B ARG 3.3 4.7 + - - +
21B TRP* 1.3 96.0 - + - +
23B GLY* 1.3 58.8 + - - +
24B ARG 3.2 4.6 + - - +
56B PHE* 3.9 18.6 - + + -
69B VAL* 3.3 56.1 - - + -
70B ASN* 4.5 13.7 - - + +
72B LYS* 4.1 23.3 - - + -
74B MET* 3.8 14.1 - - + -
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Residues in contact with GLY 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ARG 3.1 7.7 + - - -
20B CYS 3.0 9.6 + - - -
21B TRP 2.9 1.6 + - - -
22B PHE* 1.3 77.8 - - - +
24B ARG* 1.3 65.4 + - - +
25B GLN* 3.6 3.5 + - - -
56B PHE* 6.1 0.4 - - - -
320B TRP* 6.3 0.9 - - - -
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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
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20B CYS 3.2 8.4 + - - +
21B TRP* 2.7 25.1 + - + +
22B PHE 4.4 4.0 - - - +
23B GLY* 1.3 82.7 - - - +
25B GLN* 1.3 92.7 + - - +
26B ASN* 3.6 12.0 + - - +
27B THR* 5.3 3.2 - - - +
324B GLN* 3.1 38.1 + - - +
325B ARG* 5.5 0.6 - - - +
327B VAL* 3.1 31.1 - - + +
328B ASP* 2.7 29.3 + - - -
331B GLU* 5.2 6.4 + - - +
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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