Contacts of the helix formed by residues 2 - 13 (chain O) 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 LYS 2 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1O MET* 1.3 72.9 - - - +
3O ASP* 1.3 66.8 + - - +
4O VAL 3.4 0.4 + - - -
5O PRO* 3.8 2.6 - - - +
6O GLY* 3.3 16.3 + - - -
23O HIS* 3.3 34.8 + - + +
24O ARG* 3.9 27.3 + - - +
26O GLU* 3.8 8.5 - - - -
27O GLU* 3.2 39.4 + - + +
28O LEU* 6.0 0.4 - - - +
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Residues in contact with ASP 3 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1O MET* 3.3 12.7 - - + +
2O LYS* 1.3 79.3 - - - +
4O VAL* 1.3 73.6 - - + +
6O GLY* 3.2 3.1 + - - -
7O PHE* 3.1 29.6 + - - +
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Residues in contact with VAL 4 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1O MET* 3.6 29.5 + - + -
3O ASP* 1.3 79.5 - - + +
5O PRO* 1.4 73.6 - - + +
6O GLY 3.3 0.7 + - - -
7O PHE* 3.4 7.3 + - + +
8O LEU* 3.3 30.5 + - + +
35O HIS* 4.9 3.6 - - + -
42O LEU* 3.7 32.8 - - + -
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Residues in contact with PRO 5 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1O MET 3.9 11.7 - - - +
2O LYS 3.9 0.7 - - - +
4O VAL* 1.4 94.3 - - + +
6O GLY* 1.4 55.9 + - - +
8O LEU 3.6 0.7 + - - -
9O GLN* 3.0 23.6 + - - +
18O GLN* 3.2 34.9 - - - +
26O GLU* 3.4 26.2 - - - +
35O HIS* 4.2 4.0 - - - +
37O LEU 3.8 14.8 - - - +
39O LEU* 3.6 21.2 - - + +
42O LEU* 4.0 11.9 - - + -
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Residues in contact with GLY 6 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2O LYS 3.3 6.9 + - - -
3O ASP* 3.2 7.7 + - - -
4O VAL 3.1 1.2 - - - -
5O PRO* 1.4 76.9 - - - +
7O PHE* 1.3 62.7 + - - +
9O GLN* 3.3 8.7 - - - +
10O GLN* 3.0 35.7 + - - +
18O GLN* 3.8 0.2 + - - -
23O HIS* 3.6 21.8 - - - -
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Residues in contact with PHE 7 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3O ASP* 3.1 22.8 + - - +
4O VAL* 3.7 9.0 - - + +
6O GLY* 1.3 74.7 - - - +
8O LEU* 1.3 63.4 + - + +
10O GLN* 3.4 16.7 + - + +
11O SER* 2.8 50.5 + - - -
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Residues in contact with LEU 8 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4O VAL* 3.3 22.6 + - + +
5O PRO 3.9 5.2 - - - +
6O GLY 3.3 0.2 - - - -
7O PHE* 1.3 89.9 - - + +
9O GLN* 1.4 62.4 + - - +
11O SER* 3.3 17.0 + - - +
12O GLN* 3.4 21.0 + - - +
39O LEU* 4.0 25.6 - - + +
40O GLN* 4.5 12.9 + - - +
41O VAL* 3.5 35.9 - - + +
42O LEU* 3.7 28.9 - - + +
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Residues in contact with GLN 9 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5O PRO 3.0 11.3 + - - +
6O GLY* 3.3 18.0 + - - +
8O LEU* 1.4 75.4 - - - +
10O GLN* 1.4 85.4 + - - +
12O GLN* 3.9 4.8 + - - +
13O ASN* 3.5 15.1 + - - -
14O SER* 4.1 6.1 + - - +
17O GLY* 4.2 14.5 - - - -
18O GLN* 3.5 47.8 + - + +
23O HIS* 3.7 19.2 + - - -
39O LEU* 4.2 5.1 - - - +
70O ARG* 4.2 13.2 - - - +
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Residues in contact with GLN 10 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6O GLY* 3.0 31.9 + - - +
7O PHE* 3.5 14.9 - - + +
9O GLN* 1.4 94.3 + - - +
11O SER* 1.4 64.0 + - - +
13O ASN* 3.1 25.4 + - - +
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Residues in contact with SER 11 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7O PHE* 2.8 46.9 + - - -
8O LEU* 3.3 12.4 + - - +
10O GLN* 1.4 72.9 - - - +
12O GLN* 1.4 60.8 + - - +
13O ASN* 4.6 2.1 - - - +
40O GLN* 5.5 4.5 - - - -
147W GLU 4.9 5.0 - - - +
148W VAL* 4.5 21.2 - - - +
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Residues in contact with GLN 12 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8O LEU 3.4 14.4 + - - +
9O GLN* 4.0 4.5 - - - +
11O SER* 1.4 74.7 - - - +
13O ASN* 1.4 61.5 + - - +
14O SER* 3.4 11.7 + - - +
39O LEU* 4.9 6.1 - - - +
40O GLN* 3.2 36.4 + - - +
67O PHE* 4.9 0.8 - - - -
70O ARG* 3.0 44.2 - - - +
71O VAL* 3.5 18.1 - - - +
18W ASN* 3.6 12.5 + - - -
20W ASP* 2.8 31.3 - - - +
175W PRO* 5.2 4.3 - - - +
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Residues in contact with ASN 13 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O GLN 3.5 4.4 + - - -
10O GLN* 3.1 20.3 + - - +
11O SER 4.6 1.8 - - - +
12O GLN* 1.4 78.0 - - - +
14O SER* 1.4 63.4 + - - +
15O GLY* 3.6 2.1 + - - -
20W ASP* 3.8 12.3 - - + +
175W PRO* 5.6 4.5 - - + +
176W GLY* 4.0 23.7 - - - -
177W PRO* 4.6 8.3 - - - +
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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