Contacts of the helix formed by residues 13 - 19 (chain M) in PDB entry 2ZHX
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 13 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11M GLU* 4.4 3.1 - - - -
12M ARG* 1.3 77.1 - - - +
14M TRP* 1.3 56.6 + - - -
15M ALA* 3.1 4.6 - - - +
16M ALA* 3.6 19.7 - - - +
17M ALA* 3.2 24.4 + - - +
57M PHE* 3.5 21.1 - - - -
58M ASP* 5.8 0.9 - - - -
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Residues in contact with TRP 14 (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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10M VAL* 3.6 21.5 - - + -
11M GLU* 3.1 20.4 - - + -
12M ARG 2.5 9.3 + - - -
13M GLY* 1.3 70.9 - - - -
15M ALA* 1.3 55.3 + - - +
17M ALA* 4.3 2.0 - - + -
18M LEU* 2.7 50.1 + - + +
52M ALA 4.3 1.7 + - - -
53M PHE* 3.2 50.3 - + + +
55M PHE 2.7 30.3 + - - -
57M PHE* 3.4 39.3 - + + +
60M VAL* 4.4 10.5 - - + +
124M LEU* 3.6 38.1 - - + -
152M ALA* 3.8 20.2 - - + -
156M LEU* 4.6 4.9 - - + -
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Residues in contact with ALA 15 (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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6M LEU* 4.0 9.6 - - + +
7M SER* 4.1 24.0 - - - +
10M VAL* 3.4 14.4 - - + +
12M ARG* 3.2 25.5 - - + +
13M GLY 3.2 0.8 - - - +
14M TRP* 1.3 77.6 - - - +
16M ALA* 1.3 68.3 + - - +
18M LEU 3.6 0.7 - - - -
19M GLU* 2.8 24.3 + - - +
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Residues in contact with ALA 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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13M GLY* 3.6 16.3 - - - +
15M ALA* 1.3 77.5 - - - +
17M ALA* 1.3 59.7 + - - +
19M GLU* 3.1 26.6 - - - +
20M PRO* 4.1 2.6 - - - +
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Residues in contact with ALA 17 (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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13M GLY 3.2 20.2 + - - +
14M TRP* 3.9 7.2 - - + +
16M ALA* 1.3 73.8 - - - +
18M LEU* 1.3 61.6 + - - +
19M GLU 3.1 5.4 + - - -
20M PRO* 3.3 13.2 - - - +
57M PHE* 3.7 19.1 - - + -
151M CYS* 3.9 10.7 - - - -
152M ALA* 6.3 0.2 - - - -
155M ALA* 3.6 28.7 - - + +
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Residues in contact with LEU 18 (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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6M LEU* 3.5 18.3 - - + +
10M VAL* 4.1 13.2 - - + -
14M TRP* 2.7 51.1 + - + +
15M ALA 3.6 0.7 - - - -
17M ALA* 1.3 71.5 - - - +
19M GLU* 1.3 64.4 + - - +
20M PRO* 3.4 1.1 - - - -
21M VAL* 2.9 32.4 + - + +
22M ALA 3.5 3.3 + - - -
25M VAL* 6.5 0.2 - - + -
53M PHE* 3.8 23.3 - - + -
148M VAL* 3.9 36.8 - - + +
151M CYS* 4.7 2.2 - - + -
152M ALA* 4.3 15.7 - - + +
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Residues in contact with GLU 19 (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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6M LEU* 3.9 7.2 - - + -
15M ALA 2.8 12.1 + - - +
16M ALA* 3.1 20.9 - - - +
17M ALA 3.1 2.8 - - - -
18M LEU* 1.3 74.7 - - - +
20M PRO* 1.4 59.7 - - + +
22M ALA* 2.9 28.1 + - + +
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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