Contacts of the helix formed by residues 7 - 15 (chain H) in PDB entry 1E50
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 7 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5H VAL* 3.3 6.2 - - - +
6H PRO* 1.3 82.1 - - + +
8H GLN* 1.3 63.1 + - - +
9H ARG* 3.9 5.9 + - - +
10H SER* 2.8 39.5 + - - -
11H LYS* 3.1 21.7 + - - +
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Residues in contact with GLN 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H VAL* 3.5 30.1 - - - +
5H VAL* 3.7 16.5 + - - +
6H PRO 3.9 0.8 + - - -
7H ASP* 1.3 72.6 + - - +
9H ARG* 1.3 58.5 + - - +
11H LYS* 3.1 4.3 + - - +
12H PHE* 2.8 29.1 + - - +
105H GLY 3.6 16.2 - - - +
106H VAL* 4.0 9.1 - - + +
107H CYS* 2.7 39.3 + - - +
127H PHE* 3.6 14.8 - - + -
132H ALA* 3.1 32.9 + - - +
135H GLU 4.6 0.8 + - - -
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Residues in contact with ARG 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ARG* 3.5 46.3 - - - +
13B GLU* 4.2 4.9 + - - -
129B GLU* 4.1 12.1 - - - +
7H ASP* 3.5 5.5 + - - +
8H GLN* 1.3 76.8 - - - +
10H SER* 1.3 65.5 + - - +
12H PHE* 3.0 2.6 + - - +
13H GLU* 3.0 51.3 + - + +
127H PHE* 3.4 44.9 - - + +
129H GLU* 3.0 49.5 + - - +
133H GLN* 5.9 3.4 - - - +
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Residues in contact with SER 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H ASP* 2.8 37.7 + - - +
8H GLN 3.3 0.2 - - - -
9H ARG* 1.3 79.4 - - - +
11H LYS* 1.3 63.5 + - - +
13H GLU* 3.9 5.8 - - - -
14H ASN* 2.8 48.3 + - - +
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Residues in contact with LYS 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G ASP* 3.4 17.4 + - - +
68G PRO* 5.4 0.2 - - - +
5H VAL* 3.9 26.1 - - + +
7H ASP 3.1 13.1 + - - +
8H GLN 3.5 7.2 - - - +
10H SER* 1.3 77.3 + - - +
12H PHE* 1.3 61.1 + - - +
14H ASN* 5.3 0.2 - - - -
15H GLU* 2.8 64.1 + - - +
18H PHE* 3.5 17.3 - - + -
104H ASN* 3.2 23.9 + - - +
106H VAL* 3.9 13.5 - - + -
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Residues in contact with PHE 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H GLN 2.8 13.2 + - - +
9H ARG 3.5 8.3 - - - +
11H LYS* 1.3 79.1 - - - +
13H GLU* 1.3 68.4 + - + +
18H PHE* 3.3 53.3 - + + +
19H ARG* 4.3 5.2 + - - +
22H SER* 3.5 28.2 + - - -
106H VAL* 4.0 4.0 - - + -
108H VAL* 3.8 24.0 - - + -
125H LEU* 3.6 28.9 - - + -
126H GLU* 4.5 0.4 - - - -
127H PHE* 3.6 39.0 - - + -
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Residues in contact with GLU 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ARG* 4.6 2.9 + - - -
129B GLU* 3.6 18.9 - - - +
9H ARG* 3.0 43.0 + - + +
10H SER* 4.1 5.3 - - - +
12H PHE* 1.3 88.9 - - + +
14H ASN* 1.3 60.6 + - - +
19H ARG* 2.7 37.9 + - - +
127H PHE* 6.4 0.2 - - + -
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Residues in contact with ASN 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H SER* 2.8 40.1 + - - +
11H LYS* 5.3 0.2 - - - -
13H GLU* 1.3 87.4 + - - +
15H GLU* 1.3 64.6 + - + +
16H GLU 3.6 1.9 + - - -
19H ARG* 3.5 21.3 + - - +
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Residues in contact with GLU 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H LYS* 2.8 60.8 + - + +
13H GLU 3.7 0.2 - - - -
14H ASN* 1.3 78.2 - - + +
16H GLU* 1.3 67.2 + - - +
17H PHE* 4.3 11.6 - - + +
18H PHE* 3.0 20.2 + - + +
19H ARG* 3.0 17.7 + - - +
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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