Contacts of the helix formed by residues 58 - 66 (chain C) 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 58 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C PHE 3.8 2.0 + - - -
57C ALA* 1.3 79.9 - - - +
59C ARG* 1.3 63.6 + - - +
60C ALA 3.5 1.9 + - - -
61C VAL* 3.2 18.3 + - - +
62C LEU* 3.3 18.9 + - - +
260C ARG* 4.3 6.2 + - - +
318C GLN* 3.0 40.4 + - - -
479C PRO* 4.9 0.2 - - - -
21D MSE 4.1 0.4 - - - -
22D LEU* 3.7 33.2 - - - +
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Residues in contact with ARG 59 (chain C).
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 3.8 0.2 + - - -
58C SER* 1.3 71.7 - - - +
60C ALA* 1.3 59.5 - - - +
62C LEU* 3.4 1.0 + - - -
63C GLU* 2.8 52.9 + - - +
480C GLY* 4.2 12.3 - - - +
481C LEU* 3.2 28.4 - - + +
482C PRO* 4.2 28.3 - - - +
22D LEU 3.2 17.6 + - - +
23D SER* 2.9 32.1 + - - +
24D GLN 3.9 5.2 - - - +
25D PRO* 3.2 25.7 - - - +
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Residues in contact with ALA 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C SER* 4.0 0.6 - - - -
59C ARG* 1.3 82.4 - - - +
61C VAL* 1.3 64.1 + - - +
63C GLU* 3.5 8.0 + - - +
64C ALA* 3.5 7.1 + - - +
314C VAL* 3.6 9.6 - - + +
318C GLN* 3.4 26.0 - - - +
21D MSE 4.8 1.1 + - - +
24D GLN 3.7 9.4 + - - +
26D LEU* 3.8 24.9 - - - +
29D SER* 3.5 26.9 - - - +
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Residues in contact with VAL 61 (chain C).
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* 4.6 5.8 - - + -
58C SER* 3.2 23.1 + - - +
59C ARG 3.3 0.2 - - - -
60C ALA* 1.3 75.1 - - - +
62C LEU* 1.3 68.7 + - + +
64C ALA* 2.8 20.8 + - - +
65C LEU* 3.4 4.9 + - - +
260C ARG 4.5 7.4 - - - +
261C GLY 4.3 2.2 - - - -
262C CYS* 3.8 35.7 - - + +
311C GLY* 3.7 25.3 - - - +
314C VAL* 3.8 17.0 - - + -
315C ALA* 3.8 19.1 - - + +
318C GLN* 4.6 0.7 - - - +
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Residues in contact with LEU 62 (chain C).
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* 3.7 22.2 - - + +
58C SER 3.3 18.3 + - - +
59C ARG* 3.8 2.7 - - - +
61C VAL* 1.3 79.9 - - + +
63C GLU* 1.3 63.8 + - - +
65C LEU* 2.9 29.4 + - + +
66C GLY 3.8 1.4 + - - -
480C GLY* 4.0 17.7 - - - -
481C LEU* 4.3 11.9 - - + +
66D GLY* 3.7 27.4 - - - +
67D SER 3.7 23.6 - - - +
68D SER* 5.4 2.7 - - - +
70D ASN* 3.9 26.5 - - + +
71D ASN* 5.2 7.2 - - - +
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Residues in contact with GLU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ARG* 2.8 57.9 + - - +
60C ALA 3.6 6.5 - - - +
61C VAL 3.1 0.2 + - - -
62C LEU* 1.3 73.6 - - - +
64C ALA* 1.3 58.5 + - - +
66C GLY* 4.1 6.6 + - - -
67C SER* 4.4 5.5 + - - -
481C LEU* 4.3 12.4 - - + +
25D PRO* 3.7 4.9 - - - +
26D LEU* 2.7 43.1 + - + +
27D LYS 4.0 2.6 + - - -
481D LEU* 5.3 1.4 - - - +
484D PHE* 4.0 38.3 - - + -
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Residues in contact with ALA 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ALA 3.5 7.3 + - - +
61C VAL 2.8 12.3 + - - +
63C GLU* 1.3 79.0 - - - +
65C LEU* 1.3 60.8 + - - +
66C GLY 3.3 1.1 - - - -
67C SER* 2.8 25.4 + - - -
307C HIS* 4.0 8.3 - - - +
310C ALA* 4.2 21.4 - - + +
311C GLY* 4.2 8.7 - - - +
314C VAL* 4.6 6.5 - - + -
26D LEU* 4.3 16.4 - - + +
33D VAL* 5.1 0.2 - - + -
37D ILE* 4.3 8.3 - - + -
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Residues in contact with LEU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C VAL 3.4 7.3 + - - +
62C LEU* 2.9 22.4 + - + +
64C ALA* 1.3 78.6 - - - +
66C GLY* 1.3 56.1 + - - +
67C SER 3.2 3.9 + - - +
70C ASN* 4.8 0.2 - - - +
262C CYS* 4.0 19.5 - - + -
307C HIS* 3.4 52.6 - - + +
308C ALA* 3.8 16.8 - - + -
311C GLY* 5.1 0.9 - - - -
65D LEU* 3.6 32.6 - - + +
66D GLY* 4.1 0.2 - - - -
70D ASN* 3.2 33.9 - - - +
307D HIS* 4.1 8.3 - - + +
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Residues in contact with GLY 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C LEU 3.8 5.1 + - - -
63C GLU 4.1 3.6 + - - -
64C ALA 3.3 1.2 - - - -
65C LEU* 1.3 78.0 - - - +
67C SER* 1.3 59.3 + - - +
62D LEU* 3.6 30.8 - - - +
65D LEU* 4.1 5.4 - - - +
66D GLY 4.4 2.5 - - - +
481D LEU* 2.6 36.7 - - - +
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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