Contacts of the helix formed by residues 7 - 15 (chain B) in PDB entry 1E5E
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 THR 7 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ARG 3.1 6.4 + - - +
6B MET* 1.3 74.6 - - - +
8B PRO* 1.3 65.1 - - + +
9B ALA* 3.5 9.2 + - - +
10B THR* 3.1 25.4 + - - -
11B ALA* 2.7 35.7 + - - +
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Residues in contact with PRO 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B MET 3.8 1.8 - - - +
7B THR* 1.3 90.0 - - + +
9B ALA* 1.3 61.1 + - - +
11B ALA* 4.3 0.7 - - + -
12B CYS* 3.1 26.0 + - - +
73B PHE* 6.3 0.2 - - + -
74B LEU* 4.1 16.7 - - + +
190B PRO 5.8 1.1 - - - +
191B MET* 4.0 30.2 - - + +
261B ASN* 5.0 2.0 - - - +
306B ARG* 5.9 9.6 - - - +
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Residues in contact with ALA 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B THR* 3.2 9.8 + - - +
8B PRO* 1.3 79.9 - - - +
10B THR* 1.3 63.5 + - - +
12B CYS* 3.3 17.2 - - - -
13B ILE* 4.3 8.7 - - - +
261B ASN* 3.7 34.0 + - - +
265B LYS* 5.2 2.7 - - - +
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Residues in contact with THR 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B MET* 4.0 23.3 - - + -
7B THR* 3.1 17.2 + - - -
9B ALA* 1.3 79.8 - - - +
11B ALA* 1.3 61.1 + - - +
13B ILE* 3.1 5.9 + - - +
14B HIS* 2.9 46.2 + - + +
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Residues in contact with ALA 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B MET* 3.5 22.4 - - + -
7B THR 2.7 21.3 + - - +
8B PRO 3.3 0.2 + - - -
10B THR* 1.3 70.1 - - - +
12B CYS* 1.3 67.2 + - - +
13B ILE 3.0 1.6 - - - -
15B ALA* 2.9 25.0 + - + +
70B LYS* 4.9 3.5 - - - +
73B PHE* 3.8 26.7 - - + -
74B LEU* 3.8 19.0 - - + +
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Residues in contact with CYS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PRO 3.1 13.0 + - - +
9B ALA 3.3 20.0 - - - -
11B ALA* 1.3 76.6 - - - +
13B ILE* 1.3 59.9 + - - +
70B LYS* 4.7 5.6 - - - +
74B LEU* 4.2 14.3 - - + +
191B MET* 5.2 1.6 - - + -
254B THR* 4.9 1.2 - - - +
257B LEU* 3.1 41.1 - - + +
258B SER* 3.5 33.9 + - - -
260B LEU* 4.7 2.9 - - + -
261B ASN* 4.2 18.6 - - - -
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Residues in contact with ILE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ALA 4.3 11.4 - - - +
10B THR* 3.1 6.9 + - - +
11B ALA 3.0 1.1 - - - -
12B CYS* 1.3 81.7 - - - +
14B HIS* 1.3 89.6 + - + +
15B ALA 3.8 0.4 - - - -
70B LYS* 3.8 16.9 + - - -
258B SER* 3.8 34.8 - - - +
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Residues in contact with HIS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B MET* 3.9 22.4 - - + +
10B THR* 2.9 40.1 + - + +
13B ILE* 1.3 104.0 + - + +
15B ALA* 1.3 65.7 + - - +
17B PRO* 3.5 18.8 - - - +
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B MET* 4.3 6.3 - - - -
11B ALA* 2.9 28.9 + - + +
14B HIS* 1.3 74.7 - - - +
16B ASN* 1.3 67.9 + - - +
17B PRO* 4.3 0.7 - - - -
70B LYS* 2.8 31.3 + - - +
73B PHE* 3.8 42.2 - - + -
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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