Contacts of the helix formed by residues 7 - 20 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLU* 3.3 12.8 - - - -
5G TRP* 3.5 22.4 - - - -
6G SER* 1.3 75.7 - - - +
8G TYR* 1.3 60.5 + - - -
9G LEU 3.4 2.0 - - - -
10G ASP* 3.0 11.9 + - - -
11G ASP* 2.9 29.3 + - - -
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Residues in contact with TYR 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLU* 3.7 0.8 + - - -
54B TYR* 4.6 5.5 + - - -
58B ARG* 5.9 0.3 + - - -
7G GLY* 1.3 72.1 - - - -
9G LEU* 1.3 70.5 + - + +
11G ASP* 2.9 16.3 + - + +
12G VAL* 2.8 50.0 + - + +
15G LYS* 5.9 6.5 - - - -
68G PHE* 3.4 39.6 - + + -
71G ILE* 5.8 0.9 - - + -
72G ASP* 5.1 8.1 - - - +
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Residues in contact with LEU 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A SER* 4.0 6.7 + - - +
52A SER* 3.5 25.1 - - - +
53A GLU* 3.3 23.1 + - + +
56A LEU* 5.8 3.1 - - + -
8G TYR* 1.3 81.6 - - + +
10G ASP* 1.3 65.7 + - - +
12G VAL* 3.3 5.8 + - + +
13G SER* 3.0 23.2 + - - -
65G VAL* 3.4 36.1 - - + +
68G PHE* 3.5 25.8 - - + +
69G LYS* 3.6 26.9 - - + +
72G ASP* 4.2 11.7 - - - +
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Residues in contact with ASP 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A SER* 3.6 16.1 + - - +
50A LYS* 3.8 29.0 + - - +
53A GLU* 2.9 33.0 + - - +
5G TRP* 3.4 9.2 - - - -
6G SER* 3.1 24.0 - - - +
7G GLY 3.0 15.7 + - - +
9G LEU* 1.3 76.0 - - - +
11G ASP* 1.3 56.1 + - - +
13G SER* 3.3 6.1 + - - -
14G ALA* 3.0 25.7 + - - +
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Residues in contact with ASP 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G SER* 2.9 26.4 + - - +
7G GLY 2.9 18.0 + - - +
8G TYR* 2.9 18.8 + - + +
10G ASP* 1.3 73.2 - - - +
12G VAL* 1.3 54.4 + - - +
14G ALA* 3.2 8.6 + - - +
15G LYS* 2.7 53.9 + - + +
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Residues in contact with VAL 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 5.1 6.3 - - + +
8G TYR* 2.8 48.5 + - + +
9G LEU* 3.4 11.9 - - + +
10G ASP 3.2 0.2 - - - -
11G ASP* 1.3 77.2 - - - +
13G SER* 1.3 61.6 + - - +
15G LYS* 3.2 14.7 + - + +
16G PHE* 3.1 22.3 + - - +
64G THR* 4.1 10.5 - - - +
65G VAL* 3.9 18.2 - - + -
68G PHE* 3.6 35.9 - - + -
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Residues in contact with SER 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A SER* 4.2 16.0 + - - -
9G LEU 3.0 13.1 + - - -
10G ASP* 3.3 9.8 + - - -
12G VAL* 1.3 76.3 - - - +
14G ALA* 1.3 58.5 + - - +
16G PHE* 3.4 5.2 + - - +
17G ASP* 3.0 33.7 + - - +
61G GLN* 2.8 29.7 + - - +
65G VAL* 4.3 12.8 - - - -
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Residues in contact with ALA 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ASP 3.0 13.6 + - - +
11G ASP* 3.5 12.3 - - - +
13G SER* 1.3 72.6 - - - +
15G LYS* 1.3 56.9 - - + +
17G ASP* 3.3 6.9 + - - +
18G THR* 2.6 41.3 + - - +
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Residues in contact with LYS 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 5.0 19.7 - - + -
32B ASP* 5.3 13.0 + - - +
35B ALA* 3.4 16.1 - - - +
8G TYR* 5.9 6.3 - - - -
11G ASP* 2.7 42.8 + - + +
12G VAL* 3.5 14.1 - - + +
14G ALA* 1.3 74.3 - - - +
16G PHE* 1.3 60.8 + - - +
18G THR* 3.4 17.6 - - - -
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Residues in contact with PHE 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 5.3 10.4 - - + +
34B LEU* 4.9 6.5 - - + -
35B ALA* 3.6 22.4 - - - +
38B PRO* 3.6 35.9 - - + -
12G VAL 3.1 12.1 + - - +
13G SER* 3.7 7.0 - - - +
15G LYS* 1.3 75.3 - - - +
17G ASP* 1.3 72.7 + - - +
18G THR 3.2 0.7 + - - -
19G GLY 3.2 10.0 + - - -
20G VAL* 3.3 25.2 - - + +
56G LEU 3.6 18.8 - - - -
57G TYR* 3.6 22.7 - - - -
60G ALA* 4.0 14.4 - - + -
61G GLN* 3.6 25.4 - - + -
64G THR* 4.8 15.9 - - + +
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Residues in contact with ASP 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G SER* 3.0 21.8 + - - +
14G ALA* 3.3 6.4 + - - +
16G PHE* 1.3 80.4 - - - +
18G THR* 1.3 58.5 + - - +
20G VAL* 2.9 6.0 + - - -
21G ASP* 2.5 43.5 + - - +
57G TYR* 3.8 24.5 + - - +
61G GLN* 3.1 34.9 + - - +
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Residues in contact with THR 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G ALA* 2.6 27.1 + - - +
15G LYS* 3.4 12.4 + - - -
16G PHE 3.1 0.2 - - - -
17G ASP* 1.3 79.3 - - - +
19G GLY* 1.3 61.4 + - - +
20G VAL 3.5 0.2 + - - -
21G ASP* 3.8 12.7 + - - +
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Residues in contact with GLY 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ALA* 3.2 26.2 - - - +
36B ALA* 3.5 9.3 - - - +
15G LYS 4.0 1.8 + - - -
16G PHE 3.2 5.1 + - - -
17G ASP 3.1 0.6 - - - -
18G THR* 1.3 80.0 - - - +
20G VAL* 1.3 52.0 + - - +
21G ASP 3.7 0.7 - - - -
5M TRP* 2.6 39.1 + - - -
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Residues in contact with VAL 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ALA 3.3 16.2 - - - +
38B PRO* 3.5 24.9 - - + -
16G PHE* 3.3 29.4 - - + +
17G ASP* 2.9 6.3 + - - +
19G GLY* 1.3 80.9 - - - +
21G ASP* 1.3 63.6 + - - +
22G ASN 3.1 3.4 - - - +
23G LEU* 3.1 28.4 + - + +
57G TYR* 3.2 39.1 - - + -
5M TRP* 3.6 14.8 - - + +
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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