Contacts of the helix formed by residues 39 - 49 (chain A) in PDB entry 1LC7
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 PRO 39 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLY 3.6 2.4 - - - +
38A MET* 1.3 87.8 - - + +
40A VAL* 1.3 65.7 + - - +
41A SER* 3.3 4.7 - - - +
42A VAL* 3.0 40.0 + - + +
43A LYS* 3.3 5.4 + - - +
218A TYR* 3.3 32.8 - - + +
220A ILE* 5.1 0.7 - - + -
259A ALA* 4.9 1.8 - - + -
262A ASP* 4.1 16.4 - - + +
265A TRP* 3.7 37.7 - - + -
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A MET 3.3 4.6 + - - -
39A PRO* 1.3 69.8 - - - +
41A SER* 1.3 64.8 + - - +
43A LYS* 3.2 9.9 + - - +
44A ARG* 3.2 20.1 + - - +
262A ASP* 5.1 2.6 + - - -
265A TRP* 5.1 0.8 - - - -
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Residues in contact with SER 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PRO* 4.4 10.0 - - - +
40A VAL* 1.3 77.2 - - - +
42A VAL* 1.3 58.6 + - - +
44A ARG* 3.3 7.6 + - - +
45A ALA* 2.9 30.7 + - - +
258A VAL* 3.6 23.2 + - - +
261A GLN* 6.0 0.8 - - - +
262A ASP* 4.4 13.6 + - - +
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A MET* 3.9 15.3 - - + -
39A PRO* 3.0 31.0 + - + +
41A SER* 1.3 77.9 + - - +
43A LYS* 1.3 65.2 - - - +
45A ALA* 3.2 3.0 + - - +
46A LEU* 2.9 41.6 + - + +
220A ILE* 4.7 8.1 - - + -
255A ALA* 3.9 21.7 - - + +
258A VAL* 3.9 8.1 - - + -
259A ALA* 3.8 34.8 - - + +
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Residues in contact with LYS 43 (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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38A MET* 3.7 25.8 - - + +
39A PRO 3.3 4.5 + - - +
40A VAL* 3.2 12.6 + - - +
42A VAL* 1.3 80.9 - - - +
44A ARG* 1.3 64.3 + - - +
46A LEU* 3.4 5.4 + - - +
47A ILE* 3.1 31.5 + - + +
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Residues in contact with ARG 44 (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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40A VAL 3.2 9.7 + - - +
41A SER* 3.6 11.2 - - - +
43A LYS* 1.3 79.8 - - - +
45A ALA* 1.3 57.1 + - - +
47A ILE* 3.2 5.4 + - - +
48A ASP* 2.8 44.4 + - - +
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Residues in contact with ALA 45 (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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41A SER 2.9 17.3 + - - +
42A VAL* 3.6 4.3 - - - +
44A ARG* 1.3 76.4 - - - +
46A LEU* 1.3 57.5 + - - +
48A ASP* 4.6 2.0 - - - -
49A ASN* 2.8 43.8 + - - +
254A LEU* 3.4 14.8 - - + +
255A ALA* 6.0 0.2 - - - -
258A VAL* 3.6 28.9 - - + -
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Residues in contact with LEU 46 (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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38A MET* 4.5 14.8 - - + -
42A VAL* 2.9 39.8 + - + +
43A LYS* 3.7 4.5 - - - +
45A ALA* 1.3 76.6 - - - +
47A ILE* 1.3 66.4 + - + +
49A ASN 3.6 0.3 - - - -
50A LEU* 3.1 34.9 + - + +
220A ILE* 6.3 0.2 - - + -
223A LEU* 4.4 16.2 - - + -
251A LEU* 3.7 47.2 - - + +
254A LEU* 3.8 12.3 - - + -
255A ALA* 4.5 2.7 - - + -
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Residues in contact with ILE 47 (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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43A LYS* 3.1 20.9 + - + +
44A ARG* 3.8 4.7 - - - +
46A LEU* 1.3 81.0 - - + +
48A ASP* 1.3 70.6 + - - +
49A ASN 3.5 0.2 + - - -
50A LEU* 3.7 22.7 + - + +
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Residues in contact with ASP 48 (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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44A ARG* 2.8 30.5 + - - +
45A ALA* 4.0 3.3 - - - +
47A ILE* 1.3 87.3 - - - +
49A ASN* 1.3 67.3 + - - +
50A LEU 3.5 0.9 + - - -
51A ASP* 5.3 0.9 + - - +
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Residues in contact with ASN 49 (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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45A ALA* 2.8 36.1 + - - +
46A LEU 3.6 2.5 - - - -
48A ASP* 1.3 84.9 - - - +
50A LEU* 1.3 65.3 + - - +
51A ASP* 3.2 3.1 - - - +
52A CYS* 3.0 30.9 + - + -
251A LEU* 4.3 1.9 - - - +
254A LEU* 3.9 24.3 - - + +
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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