Contacts of the helix formed by residues 7 - 20 (chain K) in PDB entry 2LPZ
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 7 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E GLU* 3.3 12.3 - - - -
5K TRP* 3.5 21.5 - - - -
6K SER* 1.3 75.8 - - - +
8K TYR* 1.3 61.2 + - - -
9K LEU 3.4 2.0 - - - -
10K ASP* 3.0 12.3 + - - -
11K ASP* 2.9 28.9 + - - -
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Residues in contact with TYR 8 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E GLU* 3.7 0.8 + - - +
54F TYR* 4.6 5.5 + - - -
58F ARG* 5.9 0.3 + - - -
7K GLY* 1.3 71.9 - - - -
9K LEU* 1.3 70.4 + - + +
11K ASP* 2.9 16.7 + - + +
12K VAL* 2.8 50.3 + - + +
15K LYS* 5.9 6.7 - - - -
68K PHE* 3.4 40.3 - + + -
71K ILE* 5.8 0.9 - - + -
72K ASP* 5.1 8.3 - - - +
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Residues in contact with LEU 9 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E SER* 4.0 5.9 + - - +
52E SER* 3.5 25.4 - - - +
53E GLU* 3.3 22.9 + - + +
56E LEU* 5.8 3.1 - - + -
8K TYR* 1.3 81.2 - - + +
10K ASP* 1.3 66.7 + - - +
12K VAL* 3.3 5.7 + - + +
13K SER* 3.0 22.7 + - - -
65K VAL* 3.4 36.3 - - + +
68K PHE* 3.5 25.1 - - + +
69K LYS* 3.6 27.1 - - + +
72K ASP* 4.2 11.4 - - - +
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Residues in contact with ASP 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E SER* 3.6 15.9 + - - +
50E LYS* 3.8 29.1 + - - +
53E GLU* 2.9 32.7 + - - +
5K TRP* 3.4 9.0 - - - -
6K SER* 3.1 24.1 - - - +
7K GLY 3.0 15.9 + - - +
9K LEU* 1.3 76.1 - - - +
11K ASP* 1.3 55.3 + - - +
13K SER* 3.3 6.6 + - - -
14K ALA* 3.0 26.2 + - - +
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Residues in contact with ASP 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K SER* 2.9 26.2 + - - +
7K GLY 2.9 17.6 + - - +
8K TYR* 2.9 18.7 + - + +
10K ASP* 1.3 73.2 - - - +
12K VAL* 1.3 54.2 + - - +
14K ALA* 3.2 8.8 + - - +
15K LYS* 2.7 54.6 + - - +
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Residues in contact with VAL 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LEU* 5.1 6.1 - - + +
8K TYR* 2.8 48.6 + - + +
9K LEU* 3.4 11.7 - - + +
10K ASP 3.2 0.2 - - - -
11K ASP* 1.3 76.4 - - - +
13K SER* 1.3 62.1 + - - +
15K LYS* 3.2 14.4 + - + +
16K PHE* 3.1 22.9 + - - +
64K THR* 4.1 10.3 - - - +
65K VAL* 3.9 17.9 - - + -
68K PHE* 3.6 35.7 - - + -
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Residues in contact with SER 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E SER* 4.2 16.1 + - - -
9K LEU 3.0 12.7 + - - -
10K ASP* 3.5 9.2 - - - -
12K VAL* 1.3 76.7 - - - +
14K ALA* 1.3 57.2 + - - +
16K PHE* 3.4 4.7 + - - +
17K ASP* 3.0 33.9 + - - +
61K GLN* 2.8 29.5 + - - +
65K VAL* 4.3 12.8 - - - -
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Residues in contact with ALA 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K ASP 3.0 13.8 + - - +
11K ASP* 3.5 12.1 - - - +
13K SER* 1.3 73.4 - - - +
15K LYS* 1.3 58.1 + - + +
17K ASP* 3.3 7.0 + - - +
18K THR* 2.6 40.6 + - - +
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Residues in contact with LYS 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F THR* 6.4 0.2 - - - +
31F LEU* 5.0 19.1 - - + -
32F ASP* 5.3 12.2 + - - +
35F ALA* 3.4 16.2 - - - +
8K TYR* 5.9 6.7 - - - -
11K ASP* 2.7 41.5 + - + +
12K VAL* 3.5 14.1 - - + +
14K ALA* 1.3 75.2 - - + +
16K PHE* 1.3 61.6 + - - +
18K THR* 3.4 18.3 - - - -
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Residues in contact with PHE 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F LEU* 5.3 10.4 - - + +
34F LEU* 4.9 6.5 - - + -
35F ALA* 3.6 21.6 - - - +
38F PRO* 3.6 34.8 - - + -
12K VAL* 3.1 12.9 + - + +
13K SER* 3.7 7.4 - - - +
15K LYS* 1.3 74.7 - - - +
17K ASP* 1.3 73.0 + - - +
18K THR 3.2 0.7 + - - -
19K GLY 3.2 10.4 + - - -
20K VAL* 3.3 26.0 - - + +
56K LEU 3.6 18.8 - - - -
57K TYR* 3.6 22.7 - - - -
60K ALA* 4.0 14.6 - - + -
61K GLN* 3.6 24.7 - - + -
64K THR* 4.8 15.9 - - + +
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Residues in contact with ASP 17 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K SER* 3.0 21.8 + - - +
14K ALA* 3.8 6.5 - - - +
16K PHE* 1.3 79.8 - - - +
18K THR* 1.3 59.0 + - - +
20K VAL* 2.9 6.4 + - - -
21K ASP* 2.5 43.2 + - - +
57K TYR* 3.8 24.6 + - - +
61K GLN* 3.1 35.6 + - - +
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Residues in contact with THR 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K ALA* 2.6 27.1 + - - +
15K LYS* 3.4 12.9 + - - -
16K PHE 3.1 0.4 - - - -
17K ASP* 1.3 78.8 - - - +
19K GLY* 1.3 60.9 + - - +
21K ASP* 3.8 12.8 + - - +
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Residues in contact with GLY 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F ALA* 3.2 26.2 - - - -
36F ALA* 3.5 8.9 - - - +
15K LYS 4.0 2.0 + - - -
16K PHE 3.2 4.8 + - - -
17K ASP 3.1 0.8 - - - -
18K THR* 1.3 79.5 - - - +
20K VAL* 1.3 51.2 + - - +
21K ASP 3.7 0.7 - - - -
5Q TRP* 2.6 39.6 + - - -
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Residues in contact with VAL 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F ALA 3.3 15.9 - - - +
38F PRO* 3.5 24.9 - - + -
16K PHE* 3.3 29.2 - - + +
17K ASP* 3.1 5.8 - - - +
19K GLY* 1.3 81.7 - - - +
21K ASP* 1.3 63.0 + - - +
22K ASN 3.1 3.4 - - - +
23K LEU* 3.1 28.7 + - + +
57K TYR* 3.2 39.1 - - + -
5Q TRP* 3.6 15.3 - - + +
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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
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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