Contacts of the helix formed by residues 45 - 53 (chain F) in PDB entry 1L3B
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 45 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7F PHE* 4.4 2.5 - - - -
42F CYS 2.5 17.9 + - - -
44F THR* 1.3 72.7 - - - +
46F GLY* 1.3 65.0 + - - +
47F VAL 3.4 2.0 - - - -
48F THR* 3.3 6.2 + - - -
49F LEU* 2.8 30.3 + - - +
71F THR* 3.1 29.5 + - - +
74F ASN* 5.8 2.0 - - - -
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Residues in contact with GLY 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F PHE* 3.7 22.4 - - - -
16F PRO* 5.5 3.1 - - - +
17F THR* 4.9 2.9 - - - -
22F ARG* 3.9 22.9 + - - -
42F CYS 4.0 1.8 + - - -
44F THR* 3.4 5.9 + - - +
45F GLY* 1.3 79.3 - - - +
47F VAL* 1.3 62.8 + - - +
49F LEU* 3.6 3.9 - - - +
50F GLU* 3.4 21.0 + - - +
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Residues in contact with VAL 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F THR* 4.2 16.1 + - + +
22F ARG* 4.4 7.8 - - + +
25F ILE* 4.4 26.5 - - + -
26F MSE 4.9 4.9 - - - -
39F ASP* 3.2 29.2 - - - +
42F CYS* 5.0 3.7 + - - +
45F GLY 3.4 0.2 - - - -
46F GLY* 1.3 70.7 - - - +
48F THR* 1.3 67.6 + - - +
50F GLU* 2.9 18.1 + - - +
51F LEU* 2.9 29.4 + - + +
105F VAL* 4.1 19.5 - - + -
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Residues in contact with THR 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F ASP* 3.4 13.8 + - - -
42F CYS* 3.1 28.6 - - - +
45F GLY 3.3 7.9 + - - -
47F VAL* 1.3 76.1 - - - +
49F LEU* 1.3 54.4 + - - +
51F LEU* 3.9 1.5 - - - +
52F ALA* 2.8 37.6 + - - +
58F VAL* 4.2 9.5 - - + +
60F ALA* 3.6 9.4 - - + +
71F THR* 3.4 26.5 - - + -
75F LEU* 4.1 5.6 - - + -
84F VAL* 3.9 25.6 - - + -
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Residues in contact with LEU 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F ILE* 4.6 5.8 - - + -
7F PHE* 4.7 10.5 - - + -
45F GLY 2.8 20.5 + - - +
46F GLY 3.6 4.7 - - - +
48F THR* 1.3 75.4 - - - +
50F GLU* 1.3 70.5 + - - +
52F ALA* 3.5 11.0 - - + +
53F GLY* 3.5 4.9 + - - -
71F THR* 6.2 0.2 - - + -
74F ASN* 3.9 29.4 - - + +
75F LEU* 3.8 20.2 - - + +
78F HIS* 3.3 51.8 - - + +
80F LEU* 5.5 6.5 - - + +
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Residues in contact with GLU 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MSE 3.3 48.2 - - + +
2F ILE* 6.1 0.7 - - - +
22F ARG* 4.2 10.4 + - + +
26F MSE 3.3 35.2 - - + +
46F GLY 3.4 14.1 + - - +
47F VAL* 2.9 6.9 + - - +
49F LEU* 1.3 88.4 - - + +
51F LEU* 1.3 63.7 + - - +
53F GLY* 3.3 9.7 + - - -
54F ARG* 3.8 16.8 + - - +
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Residues in contact with LEU 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F MSE 3.7 17.0 - - + -
29F ALA* 4.6 2.5 - - + -
31F PRO* 4.0 20.0 - - + -
37F ALA* 4.0 23.3 - - + -
38F VAL 5.3 1.6 - - - +
39F ASP* 3.8 21.1 - - - +
47F VAL* 2.9 21.5 + - + +
48F THR 4.0 2.0 - - - +
50F GLU* 1.3 75.7 - - - +
52F ALA* 1.3 64.6 + - - +
54F ARG* 2.9 13.3 + - - -
55F VAL* 3.1 37.1 + - + +
58F VAL* 3.8 14.1 - - + -
103F ILE* 4.3 12.3 - - + -
105F VAL* 4.1 15.7 - - + -
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Residues in contact with ALA 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F THR 2.8 23.9 + - - +
49F LEU* 3.5 6.7 - - + +
50F GLU 3.2 0.2 - - - -
51F LEU* 1.3 73.3 - - - +
53F GLY* 1.3 59.0 + - - +
54F ARG 2.9 6.1 + - - -
55F VAL 3.6 4.0 + - - +
58F VAL* 3.9 11.1 - - - +
75F LEU* 3.9 11.2 - - + -
80F LEU* 4.0 10.5 - - + +
83F ASN* 3.1 28.0 + - - +
84F VAL* 3.7 24.9 - - + -
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Residues in contact with GLY 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LYS* 4.9 4.3 + - - -
49F LEU 3.5 4.7 + - - -
50F GLU 3.3 8.6 + - - -
51F LEU 3.3 1.0 - - - -
52F ALA* 1.3 77.3 - - - +
54F ARG* 1.3 64.4 + - - +
55F VAL 5.4 0.4 - - - -
80F LEU* 3.5 25.3 - - - +
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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