Contacts of the helix formed by residues 10 - 22 (chain B) in PDB entry 2L29
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 10 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B LEU 3.1 1.4 + - - -
9B CYS* 1.3 72.9 - - - +
11B GLY* 1.3 56.9 + - - +
12B GLU 3.6 0.4 - - - -
13B LEU* 3.3 13.1 + - - +
14B VAL* 2.7 43.6 + - - +
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Residues in contact with GLY 11 (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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1570A THR* 3.5 21.2 - - - +
8B LEU* 3.4 22.4 + - - +
9B CYS 3.4 4.4 + - - -
10B GLY* 1.3 70.3 - - - +
12B GLU* 1.3 56.9 + - - +
14B VAL* 3.9 1.5 - - - +
15B ASP* 2.9 33.8 + - - +
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Residues in contact with GLU 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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1570A THR* 5.8 0.2 - - - +
1572A ILE* 5.1 12.8 - - + +
1597A PRO 4.1 2.9 - - - +
1599A PRO* 3.2 37.8 - - + +
3B ARG* 3.9 23.1 + - - -
5B SER 4.3 0.7 - - - +
6B GLU 3.2 19.2 - - - +
7B THR* 4.5 1.3 - - - -
8B LEU* 2.7 50.3 + - + +
11B GLY* 1.3 71.5 - - - -
13B LEU* 1.3 54.7 + - - +
15B ASP* 4.6 3.8 - - - -
16B THR* 2.7 41.8 + - - +
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Residues in contact with LEU 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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8B LEU 3.6 3.2 + - - +
9B CYS* 4.3 6.5 - - + -
10B GLY* 3.5 23.8 - - - +
11B GLY 3.2 0.4 - - - -
12B GLU* 1.3 78.1 - - - +
14B VAL* 1.3 60.4 + - - +
16B THR* 2.9 20.2 + - - +
17B LEU* 3.2 16.9 - - + +
28B PHE* 4.8 11.7 - - + -
42B ILE* 3.9 28.5 - - + +
43B VAL* 3.7 30.3 - - + +
46B CYS* 3.7 38.8 - - + +
47B CYS* 4.1 1.1 - - + +
56B LEU* 6.3 1.3 - - + -
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Residues in contact with VAL 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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1570A THR* 5.2 4.5 - - + -
10B GLY* 2.7 32.6 + - - +
11B GLY* 3.9 4.9 - - - +
13B LEU* 1.3 72.7 - - + +
15B ASP* 1.3 63.0 + - + +
17B LEU* 3.3 4.9 + - - +
18B GLN* 2.9 30.7 + - + +
26B PHE* 4.1 25.6 - - + -
28B PHE* 4.5 17.3 - - + -
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Residues in contact with ASP 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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1567A PHE* 5.1 0.5 - - - +
1569A GLN* 2.8 43.7 + - - +
1570A THR* 2.6 40.5 + - + +
1572A ILE* 3.4 20.4 - - + +
11B GLY 2.9 20.8 + - - +
12B GLU 4.3 0.7 - - - +
14B VAL* 1.3 80.0 - - - +
16B THR* 1.3 51.5 + - - +
18B GLN* 3.2 7.3 + - - +
19B PHE* 2.7 36.2 + - - +
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Residues in contact with THR 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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1572A ILE* 5.5 5.2 - - + -
1599A PRO* 3.8 33.9 - - + -
1600A SER* 5.7 2.2 - - - +
1606A TYR* 5.1 3.6 - - - +
12B GLU* 2.7 26.8 + - - +
13B LEU* 2.9 14.0 + - - +
15B ASP* 1.3 73.1 - - - +
17B LEU* 1.3 68.4 + - - +
19B PHE* 3.3 14.6 + - - +
20B VAL* 3.3 20.3 + - - +
53B LEU* 5.9 2.2 - - + -
56B LEU* 4.2 25.8 - - + +
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Residues in contact with LEU 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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13B LEU* 3.2 20.5 + - + +
14B VAL* 3.5 10.3 - - - +
15B ASP 3.2 0.2 - - - -
16B THR* 1.3 85.5 + - - +
18B GLN* 1.3 55.9 + - - +
21B CYS* 2.8 39.6 + - - +
26B PHE* 3.7 21.5 - - + -
28B PHE* 3.7 23.3 - - + -
42B ILE* 3.6 27.6 - - + -
56B LEU* 4.3 19.1 - - + +
60B CYS* 3.6 39.5 - - - +
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Residues in contact with GLN 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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1543A SER* 3.6 7.1 - - - -
1545A SER* 3.7 33.3 + - - +
1569A GLN* 3.3 35.2 - - - +
14B VAL* 2.9 20.0 + - + +
15B ASP* 3.7 5.3 + - - +
17B LEU* 1.3 76.0 - - - +
19B PHE* 1.3 65.2 + - - +
22B GLY* 3.0 19.8 + - - -
26B PHE* 3.7 39.6 - - + -
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Residues in contact with PHE 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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1542A TYR* 3.5 38.9 - + - -
1543A SER* 2.7 32.0 + - - -
1567A PHE* 3.4 43.7 - + - -
1569A GLN* 4.4 13.7 - - - +
1606A TYR* 6.1 4.7 - + - -
1629A LEU* 3.7 27.6 - - + -
15B ASP* 2.7 25.6 + - - +
16B THR* 3.5 10.8 - - + +
17B LEU 3.2 0.2 - - - -
18B GLN* 1.3 75.5 - - - +
20B VAL* 1.3 69.9 + - + +
22B GLY 4.1 1.2 + - - -
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Residues in contact with VAL 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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1629A LEU* 6.5 0.2 - - + -
1631A LYS* 5.0 18.8 - - + +
16B THR 3.3 12.2 + - - +
19B PHE* 1.3 90.5 - - + +
21B CYS* 1.3 74.4 + - - +
22B GLY 3.4 1.9 + - - -
23B ASP* 4.8 2.9 + - - +
24B ARG* 4.9 4.0 + - - +
53B LEU* 5.3 5.6 - - + -
56B LEU* 4.7 14.1 - - + -
57B GLU* 5.0 15.5 - - + +
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Residues in contact with CYS 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 LEU* 2.8 25.9 + - - +
20B VAL* 1.3 93.0 - - - +
22B GLY* 1.3 57.5 + - - +
23B ASP 3.2 3.6 - - - -
24B ARG* 3.8 4.9 - - - -
25B GLY* 2.7 40.4 + - - +
26B PHE* 3.8 8.5 + - + -
56B LEU* 4.9 2.7 - - - -
57B GLU* 5.0 1.6 - - - -
60B CYS* 2.0 57.0 - - - -
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Residues in contact with GLY 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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1543A SER* 5.0 0.2 - - - -
1544A LYS* 3.7 31.1 + - - +
1545A SER* 5.6 1.6 - - - -
18B GLN* 3.0 23.5 + - - -
19B PHE 4.1 1.9 + - - -
20B VAL 3.4 2.6 - - - -
21B CYS* 1.3 78.3 - - - +
23B ASP* 1.3 60.4 + - - +
25B GLY* 4.2 2.8 + - - -
26B PHE* 4.6 10.6 - - - -
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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
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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