Contacts of the helix formed by residues 67 - 72 (chain D) in PDB entry 1EJI
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 SER 67 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C ILE* 3.6 28.2 - - - +
62C LEU* 3.7 8.2 - - - +
484C PHE* 4.3 15.7 - - - -
64D ALA 2.8 23.0 + - - -
65D LEU 3.2 1.6 - - - -
66D GLY* 1.3 83.4 - - - +
68D SER* 1.3 63.3 + - - +
69D LEU* 3.1 28.5 + - - +
70D ASN* 3.4 17.5 + - - +
307D HIS* 4.4 1.0 - - - +
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Residues in contact with SER 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ILE* 3.8 14.2 + - - +
40C GLU* 4.2 2.9 - - - +
41C SER* 3.8 5.7 + - - -
44C GLN* 3.5 29.9 + - - -
62C LEU* 5.4 4.3 - - - -
484C PHE* 3.4 34.3 + - - +
67D SER* 1.3 70.9 - - - +
69D LEU* 1.3 61.2 + - - +
70D ASN* 3.0 3.8 - - - -
71D ASN* 2.9 35.5 + - - +
72D LYS 4.2 0.9 + - - -
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Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ILE* 5.9 3.8 - - + +
37C ILE* 3.8 21.8 - - + -
40C GLU* 4.3 16.4 - - + -
44C GLN* 5.2 0.9 - - - +
263C ARG* 5.2 0.7 + - - -
67D SER* 3.1 17.7 - - - +
68D SER* 1.3 74.5 + - - +
70D ASN* 1.3 57.0 + - - +
71D ASN 2.9 11.8 + - - -
72D LYS* 3.2 15.2 + - - +
88D PHE 6.1 0.7 - - - +
89D ILE* 3.4 30.1 - - + -
92D LEU* 3.6 18.2 - - + -
306D ASN* 3.9 17.4 + - + +
307D HIS* 3.8 14.7 + - - +
310D ALA* 3.4 33.2 - - + -
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Residues in contact with ASN 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C ALA* 4.5 1.6 - - - +
62C LEU* 3.9 14.7 - - + +
65C LEU* 3.2 26.7 - - + +
256C HIS* 5.9 1.4 - - - +
261C GLY 4.2 3.4 + - - -
262C CYS* 3.6 28.2 - - - +
263C ARG* 3.4 24.4 + - - +
67D SER 3.4 15.7 + - - +
68D SER 3.0 0.6 - - - -
69D LEU* 1.3 78.2 - - - +
71D ASN* 1.3 64.7 + - - +
72D LYS 3.7 0.2 - - - -
307D HIS* 3.2 38.2 + - + +
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Residues in contact with ASN 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C GLN* 3.9 16.1 - - - +
54C GLU* 3.4 22.9 - - - +
55C ASN 3.4 23.3 + - - +
56C PHE* 3.5 16.0 - - + +
57C ALA* 3.3 40.4 + - - +
62C LEU* 5.2 4.8 - - - +
261C GLY 5.3 0.8 + - - -
263C ARG* 4.6 3.8 + - - -
479C PRO 5.4 2.4 - - - +
68D SER* 2.9 18.3 + - - +
69D LEU 2.9 1.2 - - - -
70D ASN* 1.3 87.3 + - - +
72D LYS* 1.3 58.7 + - - +
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Residues in contact with LYS 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C GLU* 4.6 8.5 - - - +
43C ARG* 3.5 22.8 - - - +
44C GLN* 5.4 2.2 - - - +
49C GLU* 4.4 2.0 + - - -
51C ILE* 3.9 8.7 - - - +
54C GLU* 3.0 22.6 + - - +
263C ARG* 3.1 17.2 + - - -
383C ALA* 5.5 0.4 - - - +
68D SER 4.2 1.1 + - - +
69D LEU* 3.2 10.3 + - - +
70D ASN 3.7 0.2 - - - -
71D ASN* 1.3 79.8 - - - +
73D TYR* 1.3 80.0 + - - +
74D SER* 4.9 0.2 - - - -
83D TYR* 4.8 0.2 - - - +
84D GLY 2.6 31.0 + - - +
85D GLY 3.7 15.0 - - - +
86D THR* 4.1 5.4 - - - -
89D ILE* 3.5 36.1 - - + -
304D PRO 4.6 0.3 - - - +
306D ASN* 3.1 19.0 + - - +
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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