Contacts of the helix formed by residues 2 - 21 (chain B) in PDB entry 2LP3
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 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 6.0 0.4 - - - -
18A HIS* 5.6 3.1 - - - -
39A THR* 5.0 3.8 + - - -
40A GLU* 3.1 49.9 + - - +
1B GLY* 1.3 83.3 - - - +
3B GLU* 1.3 65.8 + - - +
4B LEU 3.5 2.1 + - - -
5B GLU* 3.1 24.2 + - - +
6B THR* 3.5 7.0 + - - -
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Residues in contact with GLU 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR* 3.5 24.6 - - + +
13A ASN* 4.3 11.3 + - - +
14A VAL* 3.5 23.5 + - + +
1B GLY 5.7 0.2 - - - +
2B SER* 1.3 74.1 - - - +
4B LEU* 1.3 58.9 + - - +
6B THR* 3.0 13.7 + - - -
7B ALA* 2.8 25.1 + - - +
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Residues in contact with LEU 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR* 4.8 1.8 - - - -
11A LEU* 3.0 37.2 - - + -
14A VAL* 4.2 13.5 - - + +
37A LEU* 5.6 0.2 - - + -
40A GLU* 2.7 36.6 - - + +
41A LEU* 3.5 24.2 - - + -
74A TYR* 4.1 19.3 - - + +
78A VAL* 4.6 16.6 - - + -
2B SER* 3.2 2.3 + - - +
3B GLU* 1.3 79.1 - - - +
5B GLU* 1.3 63.3 + - - +
7B ALA* 2.9 6.4 + - + +
8B MET* 2.9 30.2 + - + +
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Residues in contact with GLU 5 (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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40A GLU 4.0 19.2 + - - +
41A LEU* 5.4 0.2 - - - -
44A PHE* 4.6 17.3 - - + -
1B GLY* 2.7 31.4 + - - -
2B SER* 3.1 14.3 + - - +
4B LEU* 1.3 79.7 - - - +
6B THR* 1.3 63.5 + - - +
8B MET* 3.5 19.5 + - + +
9B GLU* 3.4 35.3 + - - +
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Residues in contact with THR 6 (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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1B GLY 5.2 1.6 + - - -
2B SER 3.5 9.4 + - - -
3B GLU* 3.0 13.2 + - - -
5B GLU* 1.3 80.6 - - - +
7B ALA* 1.3 49.6 + - - +
9B GLU* 3.2 14.9 + - + +
10B THR* 2.6 43.1 + - - +
13B ASN* 5.0 0.2 + - - -
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Residues in contact with ALA 7 (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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7A ALA* 4.6 9.2 - - + -
10A THR* 4.2 18.4 - - + -
11A LEU* 4.2 17.7 - - + -
3B GLU 2.8 11.9 + - - +
4B LEU* 2.9 14.3 + - + +
6B THR* 1.3 74.9 - - - +
8B MET* 1.3 65.5 + - - +
10B THR* 2.8 20.8 + - - -
11B LEU* 2.9 21.4 + - + +
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Residues in contact with MET 8 (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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41A LEU* 3.5 40.4 - - + -
44A PHE* 4.4 20.9 - - + -
78A VAL* 5.5 7.0 - - + +
82A THR* 3.5 42.6 + - - +
85A CYS* 4.5 13.5 - - + -
4B LEU* 2.9 25.2 + - + +
5B GLU* 3.9 18.6 - - + +
6B THR 3.4 0.2 - - - -
7B ALA* 1.3 76.5 - - - +
9B GLU* 1.3 66.4 + - + +
11B LEU* 3.4 16.6 + - + +
12B ILE* 3.4 20.6 + - - +
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Residues in contact with GLU 9 (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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44A PHE* 5.6 5.9 - - + -
5B GLU* 3.4 30.1 + - + +
6B THR* 3.2 15.3 + - + +
7B ALA 3.1 0.2 - - - -
8B MET* 1.3 79.7 - - + +
10B THR* 1.3 52.3 + - - +
12B ILE* 3.3 8.9 + - + +
13B ASN* 2.4 54.2 + - - +
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Residues in contact with THR 10 (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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3A GLU* 3.5 47.8 - - + +
4A LEU* 4.4 1.3 - - - +
7A ALA* 4.2 11.4 - - + +
6B THR* 2.6 35.1 + - - +
7B ALA* 2.8 13.3 + - - -
9B GLU* 1.3 77.4 - - - +
11B LEU* 1.3 56.1 + - - +
13B ASN* 3.6 7.7 + - - +
14B VAL* 2.9 36.6 + - + +
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Residues in contact with LEU 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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4A LEU* 3.0 34.5 - - + -
7A ALA* 4.2 11.9 - - + -
11A LEU* 5.7 10.8 - - + -
79A ALA* 6.1 1.8 - - - -
82A THR* 4.7 17.0 - - + +
7B ALA* 2.9 16.1 + - + +
8B MET* 3.6 14.1 - - + +
9B GLU 3.3 0.2 - - - -
10B THR* 1.3 76.3 - - - +
12B ILE* 1.3 59.2 + - + +
14B VAL* 2.9 23.6 - - - +
15B PHE* 2.9 14.8 + - - +
71B PHE* 4.6 14.1 - - + -
75B VAL* 6.1 2.9 - - + -
78B VAL* 5.4 14.1 - - + -
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Residues in contact with ILE 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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82A THR* 4.3 13.0 - - - +
83A VAL* 6.1 0.2 - - - -
85A CYS* 4.4 5.6 - - - -
86A ASN* 2.9 42.4 - - - +
8B MET 3.5 15.3 - - - +
9B GLU* 3.3 9.3 + - + +
10B THR 3.3 0.2 - - - -
11B LEU* 1.3 75.5 - - + +
13B ASN* 1.3 61.5 + - - +
15B PHE* 3.5 10.9 - - + +
16B HIS* 2.7 39.1 + - + +
71B PHE* 4.9 12.1 - - + -
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Residues in contact with ASN 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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3A GLU* 4.3 9.8 + - - +
9B GLU* 2.4 50.0 + - - +
10B THR* 3.2 9.3 + - - +
12B ILE* 1.3 77.8 - - - +
14B VAL* 1.3 61.3 + - - +
16B HIS* 3.9 5.6 - - - +
17B ALA* 3.5 19.4 + - - +
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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
----------------------------------------------------------
2A SER* 6.0 0.4 - - - -
3A GLU* 3.5 37.5 - - + +
4A LEU* 4.2 16.2 - - + +
10B THR 2.9 19.6 + - - +
11B LEU* 2.9 28.9 - - - +
13B ASN* 1.3 74.0 - - - +
15B PHE* 1.3 66.8 + - - +
17B ALA* 3.3 3.6 + - - +
18B HIS* 2.8 37.9 + - + +
36B LEU* 5.9 0.7 - - + -
40B GLU* 3.8 25.1 - - - +
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Residues in contact with PHE 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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11B LEU 2.9 19.5 + - - +
12B ILE* 3.5 11.4 - - + +
14B VAL* 1.3 80.4 - - + +
16B HIS* 1.3 61.0 + - + +
18B HIS* 4.9 2.5 - - - -
19B SER* 2.8 52.5 + - - +
25B LYS 2.6 34.3 - - - -
26B TYR* 3.9 16.4 - + - -
27B LYS 4.4 3.4 - - - -
28B LEU* 3.6 25.4 - - + -
36B LEU* 5.0 6.3 - - + -
71B PHE* 3.0 58.1 - + + -
74B TYR* 5.5 1.1 - + - -
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Residues in contact with HIS 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 ILE* 2.7 24.4 + - + +
13B ASN* 3.9 6.5 - - - +
15B PHE* 1.3 80.9 - - + +
17B ALA* 1.3 66.0 + - - +
19B SER* 5.1 0.7 - - - -
20B GLY 3.4 13.3 + - - -
25B LYS* 3.2 55.9 + - + +
26B TYR* 5.1 7.6 - + - -
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Residues in contact with ALA 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 ASN 3.5 10.6 + - - +
14B VAL* 3.3 7.9 + - - +
15B PHE 3.3 0.4 - - - -
16B HIS* 1.3 86.7 + - - +
18B HIS* 1.3 70.9 + - + +
20B GLY* 3.5 6.4 + - - -
21B LYS* 3.8 13.0 + - - +
25B LYS* 5.6 0.4 - - - +
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Residues in contact with HIS 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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2A SER* 5.6 2.8 - - - -
14B VAL* 2.8 33.2 + - + +
15B PHE 4.3 0.4 - - - +
17B ALA* 1.3 79.0 - - + +
19B SER* 1.3 66.8 + - - +
21B LYS* 3.0 51.5 + - - +
32B GLU* 3.9 7.2 - - + +
36B LEU* 3.0 42.0 - - + +
39B THR* 5.1 11.0 - - + -
40B GLU* 3.1 20.5 + - + +
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Residues in contact with SER 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 PHE* 2.8 49.8 + - - -
18B HIS* 1.3 74.6 - - - +
20B GLY* 1.3 56.2 + - - +
22B GLU 2.7 7.3 - - - +
23B GLY 4.3 0.3 - - - +
24B ASP 4.0 0.9 - - - +
25B LYS* 2.9 28.2 - - - -
27B LYS 4.3 0.7 - - - -
28B LEU* 4.2 3.5 - - - +
32B GLU* 2.6 23.7 + - - +
36B LEU* 5.0 0.5 - - - +
101B CA 2.5 25.0 - - - -
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Residues in contact with GLY 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 HIS 3.4 8.9 + - - -
17B ALA 3.9 2.9 - - - -
18B HIS 3.1 1.6 - - - -
19B SER* 1.3 77.2 - - - +
21B LYS* 1.3 66.7 + - - +
22B GLU* 3.2 3.6 + - - -
23B GLY 4.5 4.6 - - - +
25B LYS* 3.7 36.0 + - - +
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Residues in contact with LYS 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 ALA 3.8 9.6 + - - +
18B HIS* 3.0 44.8 + - - +
20B GLY* 1.3 78.6 - - - +
22B GLU* 1.3 71.0 + - + +
31B LYS* 6.5 1.1 - - - +
32B GLU* 4.5 8.3 - - + +
35B GLU* 4.6 18.7 - - - +
36B LEU* 5.4 1.2 - - - +
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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