Contacts of the helix formed by residues 8 - 16 (chain M) in PDB entry 5G04
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 ASP 8 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C LYS* 5.7 2.9 + - - -
128C LYS* 4.0 15.8 + - - -
6M GLN 3.5 2.6 + - - -
7M ARG* 1.3 70.7 - - - +
9M GLY* 1.3 69.5 + - - +
10M ARG* 3.5 22.8 + - - +
11M ILE* 3.1 33.1 + - + +
12M LEU* 2.9 19.6 + - - +
97P LYS* 5.0 15.9 + - - +
128P LYS* 5.7 0.4 - - - +
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Residues in contact with GLY 9 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M ARG 3.1 5.5 + - - -
8M ASP* 1.3 73.7 + - - +
10M ARG* 1.3 52.0 + - - +
12M LEU* 2.9 9.4 + - - +
13M ASP* 2.6 38.9 + - - +
329P TYR* 3.8 29.7 - - - +
360P LEU* 4.0 16.0 - - - +
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Residues in contact with ARG 10 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C LYS* 4.9 10.5 - - - +
131C ASP* 4.1 38.8 + - + +
132C ASP* 5.2 4.0 - - - +
135C VAL* 4.1 22.9 - - + +
8M ASP* 3.4 17.1 + - - +
9M GLY* 1.3 70.9 - - - +
11M ILE* 1.3 85.7 + - - +
13M ASP* 3.2 9.2 + - - +
14M LEU* 3.0 42.2 + - - +
329P TYR* 4.0 14.0 - - + +
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Residues in contact with ILE 11 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C TYR* 4.3 21.8 - - + +
360C LEU* 5.5 7.9 - - + -
8M ASP* 3.1 35.9 + - + +
10M ARG* 1.3 107.9 - - - +
12M LEU* 1.3 65.9 + - - +
14M LEU* 3.1 19.6 + - + +
15M ILE* 3.4 31.2 + - + +
20M ARG* 5.4 1.3 - - - +
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Residues in contact with LEU 12 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7M ARG* 3.6 39.0 - - + +
8M ASP 2.9 15.0 + - - +
9M GLY* 3.3 17.7 - - - +
11M ILE* 1.3 73.9 - - - +
13M ASP* 1.3 68.1 + - + +
15M ILE* 3.5 12.6 + - - +
16M ASP* 4.2 5.4 + - - -
17M ASP* 4.8 6.1 - - - +
20M ARG* 4.1 14.3 + - - +
329P TYR* 4.9 4.7 - - + -
356P ARG* 5.2 11.2 - - + +
359P LYS* 3.4 41.3 - - + +
360P LEU* 4.4 18.8 - - + -
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Residues in contact with ASP 13 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ASP 5.5 0.2 - - - +
135C VAL* 3.3 32.1 - - + +
136C ASP* 5.3 0.3 - - - -
9M GLY 2.6 19.0 + - - +
10M ARG* 3.4 7.2 - - - +
12M LEU* 1.3 74.6 - - + +
14M LEU* 1.3 61.2 + - - +
16M ASP 4.9 2.2 + - - -
328P LYS* 4.5 2.3 + - - -
329P TYR* 2.5 38.4 + - + +
356P ARG* 5.1 9.5 + - - -
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Residues in contact with LEU 14 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C VAL* 3.9 26.0 - - + -
359C LYS* 3.6 42.6 - - + +
360C LEU* 4.1 23.1 - - + -
10M ARG* 3.0 29.5 + - - +
11M ILE* 3.1 11.2 + - + +
13M ASP* 1.3 79.3 - - - +
15M ILE* 1.3 60.2 + - + +
16M ASP* 3.7 4.1 + - - +
19M TRP* 4.1 10.5 - - + -
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Residues in contact with ILE 15 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C TYR* 3.6 30.7 - - + -
360C LEU* 5.3 3.6 - - + -
11M ILE* 3.4 29.2 - - + +
12M LEU 3.5 6.1 + - - +
13M ASP 3.5 1.4 - - - -
14M LEU* 1.3 77.6 - - + +
16M ASP* 1.3 74.6 + - - +
17M ASP* 3.1 9.9 + - - +
19M TRP* 3.5 39.5 - - + +
20M ARG* 3.5 57.0 - - + +
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Residues in contact with ASP 16 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M LEU 4.2 6.2 + - - -
13M ASP 4.9 2.2 + - - -
14M LEU 3.7 5.1 - - - +
15M ILE* 1.3 81.4 - - - +
17M ASP* 1.3 56.0 + - - +
18M ALA* 2.6 27.4 + - - +
19M TRP* 3.4 25.1 + - - +
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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