Contacts of the helix formed by residues 67 - 72 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ILE* 3.8 17.3 - - - -
62A LEU* 3.8 7.6 - - - +
484A PHE* 3.4 30.0 - - - -
64B ALA 2.8 20.9 + - - -
65B LEU 3.2 2.2 - - - -
66B GLY* 1.3 83.0 - - - +
68B SER* 1.3 62.2 + - - +
69B LEU* 3.1 28.3 + - - +
70B ASN* 3.4 17.3 + - - +
307B HIS* 4.4 1.0 - - - +
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Residues in contact with SER 68 (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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37A ILE* 3.9 4.2 + - - +
40A GLU* 4.1 2.6 - - - +
41A SER* 3.5 18.2 + - - -
44A GLN* 3.1 32.3 + - - -
62A LEU* 5.4 3.6 - - - -
484A PHE* 3.3 29.1 + - - -
67B SER* 1.3 71.1 - - - +
69B LEU* 1.3 60.3 + - - +
70B ASN 3.0 2.9 - - - -
71B ASN* 2.9 36.0 + - - +
72B LYS 4.2 0.7 + - - -
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Residues in contact with LEU 69 (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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36A ILE* 5.6 3.1 - - + +
37A ILE* 3.7 20.6 - - + -
40A GLU* 3.9 19.3 - - + -
44A GLN* 5.0 1.6 - - - +
263A ARG* 5.2 0.5 + - - -
67B SER* 3.1 19.7 - - - +
68B SER* 1.3 75.1 + - - +
70B ASN* 1.3 57.0 + - - +
71B ASN 2.9 11.0 + - - -
72B LYS* 3.2 15.0 + - - +
88B PHE 6.0 0.4 - - - +
89B ILE* 3.4 28.9 - - + -
92B LEU* 3.6 18.6 - - + -
306B ASN* 3.9 15.9 + - + +
307B HIS* 3.8 15.2 + - - +
310B ALA* 3.4 31.4 - - + -
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Residues in contact with ASN 70 (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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57A ALA* 4.5 1.6 - - - +
62A LEU* 3.9 15.1 - - + +
65A LEU* 3.3 19.4 - - + +
256A HIS* 5.8 2.2 - - - +
261A GLY 4.1 4.6 + - - -
262A CYS* 3.7 26.2 - - - +
263A ARG* 3.3 24.3 + - - +
67B SER 3.4 14.8 + - - +
68B SER 3.0 0.8 - - - -
69B LEU* 1.3 76.6 - - - +
71B ASN* 1.3 65.8 + - - +
72B LYS 3.6 0.4 - - - -
307B HIS* 3.2 45.1 + - + +
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Residues in contact with ASN 71 (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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44A GLN* 3.7 15.6 - - - +
54A GLU* 3.2 22.9 - - - +
55A ASN 3.1 27.8 + - - +
56A PHE* 3.4 24.6 - - + +
57A ALA* 3.2 29.8 + - - +
62A LEU* 5.4 4.3 - - - +
261A GLY 5.4 1.0 + - - -
263A ARG* 4.7 4.3 + - - -
479A PRO 5.4 2.4 - - - +
68B SER* 2.9 18.3 + - - +
69B LEU 2.9 0.8 - - - -
70B ASN* 1.3 88.8 + - - +
72B LYS* 1.3 60.0 + - - +
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Residues in contact with LYS 72 (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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40A GLU* 4.4 8.7 - - - +
43A ARG* 3.3 28.4 - - - +
44A GLN* 5.5 1.6 - - - +
49A GLU* 4.2 2.4 + - - -
51A ILE* 3.7 10.5 - - - +
54A GLU* 3.1 19.6 + - - +
263A ARG* 3.2 15.8 + - - -
383A ALA* 4.7 0.2 - - - +
68B SER 4.2 0.8 + - - +
69B LEU* 3.2 9.7 + - - +
70B ASN 3.6 0.2 - - - -
71B ASN* 1.3 78.6 - - - +
73B TYR* 1.3 79.8 + - - +
83B TYR* 4.5 0.8 - - - +
84B GLY 2.5 31.3 + - - -
85B GLY 3.8 10.3 - - - -
86B THR* 4.0 5.2 - - - -
89B ILE* 3.6 36.8 - - + -
304B PRO 4.6 0.5 - - - +
306B ASN* 3.1 17.3 + - - +
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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