Contacts of the helix formed by residues 10 - 16 (chain A) in PDB entry 2LHS
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 ARG 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ALA 3.8 0.6 + - - -
9A SER* 1.3 70.8 - - - +
11A ALA* 1.3 57.1 + - - +
13A GLN* 3.7 8.5 - - - +
14A CYS* 3.0 28.4 + - - +
19A ASN* 3.3 25.3 - - - +
22A CYS* 4.4 1.6 - - - -
58A GLU 2.9 25.6 + - - +
59A LEU* 3.2 36.0 + - + -
60A ASP* 3.4 3.0 + - - +
61A GLN 3.1 24.5 + - - -
62A GLN* 2.9 23.2 + - - +
67A TRP* 3.3 26.7 - - + +
107A LEU* 4.9 1.0 - - - +
146A VAL* 3.6 17.2 - - - +
163A ALA* 2.8 28.8 + - - +
165A ASP* 4.0 20.3 + - + +
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Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A TYR* 5.8 1.1 - - + -
9A SER* 3.0 13.9 + - - +
10A ARG* 1.3 79.1 - - - +
12A TYR* 1.3 63.0 + - - +
14A CYS* 3.2 18.2 + - - +
15A LYS 3.5 4.2 + - - -
25A VAL* 3.6 35.0 - - + +
29A PRO* 3.8 13.8 - - + +
32A VAL* 4.1 8.1 - - + -
59A LEU* 4.1 16.8 - - + +
160A PHE* 6.0 0.2 - - + -
162A GLN* 4.9 7.6 - - + +
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Residues in contact with TYR 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A TYR* 3.6 38.1 + + + -
4A VAL 3.8 15.7 - - - +
5A GLU* 3.4 39.3 + - + +
8A ALA* 4.1 7.9 - - + -
9A SER* 2.9 11.0 + - - +
11A ALA* 1.3 77.3 - - - +
13A GLN* 1.3 64.5 + - - +
15A LYS* 3.1 8.1 + - + +
16A LEU* 3.0 59.3 + - + +
29A PRO* 4.0 19.9 - - + +
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Residues in contact with GLN 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ALA* 3.0 32.5 + - + +
9A SER 2.8 17.9 + - - +
10A ARG* 3.7 7.0 - - - +
12A TYR* 1.3 77.6 - - - +
14A CYS* 1.3 59.5 + - - +
16A LEU* 3.2 9.2 + - - -
17A GLN 3.0 4.2 + - - -
18A LEU* 2.8 38.8 + - + +
19A ASN* 2.9 37.6 + - - +
67A TRP* 4.5 0.5 - - - +
68A ASN* 3.4 25.8 + - - +
70A LEU* 3.6 22.5 - - + +
164A ILE* 4.0 8.9 - - - +
165A ASP 4.4 1.4 + - - +
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Residues in contact with CYS 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG 3.0 8.1 + - - +
11A ALA 3.4 10.8 - - - +
12A TYR 3.2 0.4 - - - -
13A GLN* 1.3 77.4 - - - +
15A LYS* 1.3 57.3 + - - +
17A GLN* 3.0 21.1 + - - +
19A ASN* 3.4 32.5 - - - +
20A THR* 3.6 8.1 - - - -
22A CYS* 2.0 54.7 - - + -
25A VAL 4.4 0.4 - - - -
26A GLN* 3.4 22.4 - - + +
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Residues in contact with LYS 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA 3.5 1.6 + - - -
12A TYR* 3.1 14.8 + - + +
14A CYS* 1.3 74.7 - - - +
16A LEU* 1.3 61.9 + - + +
17A GLN* 3.0 18.3 + - - +
25A VAL 4.0 7.9 - - - +
26A GLN* 3.4 19.9 + - - +
27A TYR* 2.9 34.1 + - - +
29A PRO* 3.7 29.8 - - + -
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Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ALA* 4.9 7.0 - - + -
12A TYR* 3.0 59.5 + - + +
13A GLN* 3.2 9.4 + - - +
15A LYS* 1.3 78.0 - - + +
17A GLN* 1.3 67.0 + - - +
18A LEU* 3.1 33.5 + - + +
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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