Contacts of the helix formed by residues 21 - 33 (chain E) in PDB entry 5LN3
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 LEU 21 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E VAL 5.4 0.7 - - - +
14E THR 4.0 13.7 - - - +
15E PHE* 3.7 35.4 + - + +
16E SER* 3.6 6.1 - - - -
19E GLY 5.0 0.9 - - - +
20E ARG* 1.4 70.5 - - - +
22E PHE* 1.3 64.2 + - - +
23E GLN* 3.4 15.7 - - + +
24E VAL* 3.2 32.2 - - + +
25E GLU* 3.0 12.3 - - - +
123E PHE* 4.0 21.8 - - + -
126E GLU* 5.9 0.2 - - - +
126F ARG* 3.6 32.5 - - - +
437M TYR* 4.9 9.1 - - + +
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Residues in contact with PHE 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ARG* 4.4 18.2 - - - -
11E GLY 5.3 1.6 - - - -
12E VAL* 6.1 1.3 - - + -
14E THR* 3.7 21.5 + - - -
16E SER* 3.5 32.2 + - - -
17E PRO* 4.1 13.5 - - + -
18E GLU* 5.7 5.6 - - + -
20E ARG 4.4 4.3 - - - -
21E LEU* 1.3 72.6 - - - +
23E GLN* 1.3 69.4 + - + +
25E GLU* 3.2 24.1 + - - +
26E TYR* 3.3 44.5 - + + +
4F ASN* 6.3 1.8 - - - -
7F ASP* 5.1 3.4 - - - -
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Residues in contact with GLN 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D PHE* 3.5 46.0 - - + -
12E VAL* 2.9 43.4 + - + +
14E THR 5.5 0.2 + - - -
21E LEU* 3.4 12.5 - - + +
22E PHE* 1.3 83.5 - - + +
24E VAL* 1.4 61.4 + - + +
26E TYR* 3.4 12.3 + - + -
27E ALA* 3.4 11.4 + - - +
123E PHE* 4.6 16.9 - - + +
134E SER 3.8 4.6 + - - +
135E ARG* 3.8 8.1 - - - -
136E PRO* 3.5 29.9 - - + +
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Residues in contact with VAL 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ARG* 4.2 26.8 + - - +
21E LEU* 3.2 33.7 - - + +
23E GLN* 1.4 78.8 - - + +
25E GLU* 1.3 62.1 + - - +
27E ALA* 3.3 19.3 + - - +
28E ILE* 3.8 11.3 - - - +
123E PHE* 5.4 12.3 - - + -
136E PRO* 4.8 13.5 - - + -
158E PRO* 4.5 18.2 - - - +
159E SER* 4.5 17.2 + - - +
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Residues in contact with GLU 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ARG* 3.1 50.1 - - - +
21E LEU 3.0 19.8 - - - +
22E PHE* 3.2 16.2 + - - +
24E VAL* 1.3 74.1 - - - +
26E TYR* 1.4 69.8 + - + +
28E ILE* 3.4 23.7 + - - +
29E GLU* 3.9 6.1 + - - +
434M ASN* 5.6 3.3 + - - +
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Residues in contact with TYR 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D PHE* 4.0 7.9 - + + -
11D SER* 2.9 27.6 - - - +
12D PRO* 3.4 28.3 + - + +
13D ASP* 4.2 7.6 - - - -
14D GLY* 4.0 20.4 - - - +
22E PHE* 3.3 53.0 - + + +
23E GLN* 3.6 14.8 - - + +
24E VAL 3.3 0.4 - - - -
25E GLU* 1.4 79.7 - - + +
27E ALA* 1.3 63.5 + - - +
29E GLU* 3.0 23.6 + - - +
30E ALA 3.3 4.3 + - - -
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Residues in contact with ALA 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D PHE* 5.5 6.0 - - + -
23E GLN 3.4 8.4 + - - +
24E VAL* 3.3 14.8 + - - +
25E GLU 3.2 0.4 - - - -
26E TYR* 1.3 75.5 - - - +
28E ILE* 1.3 65.7 + - - +
30E ALA* 3.0 19.3 + - - +
31E ILE* 3.2 19.6 + - - +
136E PRO* 6.0 3.4 - - + -
137E PHE 4.9 2.5 - - - +
138E GLY* 4.4 19.7 - - - +
158E PRO* 4.5 16.8 - - + +
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Residues in contact with ILE 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ARG* 5.8 4.9 - - - +
24E VAL 3.8 9.9 - - - +
25E GLU* 3.5 16.4 - - - +
26E TYR 3.2 0.2 - - - -
27E ALA* 1.3 74.8 - - - +
29E GLU* 1.4 63.8 + - + +
31E ILE* 3.3 12.9 + - + +
32E LYS* 3.1 21.3 + - + +
158E PRO* 3.9 26.9 - - + -
159E SER* 5.0 7.2 - - - +
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Residues in contact with GLU 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ASP* 4.0 26.6 - - - +
14D GLY* 5.2 0.7 - - - -
25E GLU 3.9 4.7 + - - +
26E TYR* 3.0 13.7 + - + +
28E ILE* 1.4 82.6 - - + +
30E ALA* 1.4 60.8 + - - +
32E LYS* 3.4 37.6 + - - +
33E LEU* 3.6 19.6 + - - +
345H LEU* 6.2 4.9 - - + -
379H ASN* 4.2 23.8 + - - +
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Residues in contact with ALA 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D GLY* 4.6 16.3 - - - +
26E TYR 3.3 5.5 + - - +
27E ALA* 3.0 16.0 + - - +
29E GLU* 1.4 79.9 - - - +
31E ILE* 1.3 58.1 + - + +
33E LEU* 3.2 34.1 + - + +
34E GLY* 3.7 2.9 + - - -
80E GLY* 5.2 3.1 - - - -
81E LEU* 4.0 35.2 - - + +
138E GLY* 5.0 2.7 - - - +
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Residues in contact with ILE 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ALA 3.4 9.9 - - - +
28E ILE* 3.4 14.4 - - + +
30E ALA* 1.3 72.4 - - - +
32E LYS* 1.4 62.3 + - - +
33E LEU 3.1 1.8 - - - -
34E GLY* 3.0 18.0 + - - +
79E SER* 3.7 20.9 - - - +
80E GLY* 4.0 6.9 - - - -
138E GLY 3.4 28.3 - - - +
139E VAL 3.9 1.6 - - - -
140E ALA* 3.7 33.7 - - + +
158E PRO* 4.2 12.8 - - + -
170E ILE* 5.5 3.8 - - + -
171E GLY* 4.4 21.3 - - - +
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Residues in contact with LYS 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E ILE* 3.1 12.0 + - + +
29E GLU* 3.4 35.6 + - - +
31E ILE* 1.4 74.0 - - - +
33E LEU* 1.3 67.6 + - + +
171E GLY 4.6 3.4 - - - +
172E SER* 3.2 51.1 + - - +
348H LEU* 4.0 19.3 - - - +
351H ARG* 4.0 25.1 - - - +
375H ARG* 3.1 32.3 + - - +
377H CYS 4.1 6.7 + - - -
379H ASN* 4.6 8.2 - - + +
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Residues in contact with LEU 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D GLY 4.6 6.7 - - - +
15D HIS* 4.5 23.1 - - + +
29E GLU* 3.6 18.8 - - - +
30E ALA* 3.2 18.6 - - - +
31E ILE 3.1 0.4 - - - -
32E LYS* 1.3 84.0 - - + +
34E GLY* 1.3 63.7 + - - +
53E ARG* 4.3 9.0 + - - -
81E LEU* 6.3 1.8 - - + -
375H ARG 6.0 0.9 - - - +
376H LEU* 5.0 14.0 - - - +
377H CYS 5.3 2.2 - - - +
378H PRO* 5.3 13.7 - - + -
379H ASN 6.0 0.9 - - - +
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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