Contacts of the helix formed by residues 58 - 66 (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 58 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A MSE 4.0 1.1 - - - -
22A LEU* 3.8 33.7 - - - +
56B PHE 3.7 2.0 + - - -
57B ALA* 1.3 79.7 - - - +
59B ARG* 1.3 64.1 + - - +
60B ALA 3.5 1.7 + - - -
61B VAL* 3.2 20.1 + - - +
62B LEU* 3.3 18.5 + - - +
260B ARG* 4.3 6.6 + - - +
318B GLN* 3.1 37.4 + - - -
479B PRO* 4.9 0.4 - - - -
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Residues in contact with ARG 59 (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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22A LEU 3.3 9.0 + - - +
23A SER 3.0 26.2 + - - +
24A GLN 3.7 11.4 - - - +
25A PRO* 3.2 27.2 - - + +
58B SER* 1.3 71.4 - - - +
60B ALA* 1.3 60.0 + - - +
61B VAL 3.3 0.2 + - - -
62B LEU* 3.3 1.4 + - - +
63B GLU* 2.8 56.9 + - - +
480B GLY* 3.4 23.7 - - - +
481B LEU* 4.1 14.2 - - + +
482B PRO* 3.6 35.4 - - - +
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Residues in contact with ALA 60 (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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21A MSE 5.0 0.7 - - - +
24A GLN 3.6 6.4 + - - +
26A LEU* 3.6 28.7 - - + +
29A SER* 3.4 26.2 - - - +
58B SER* 3.2 1.2 + - - -
59B ARG* 1.3 80.8 - - - +
61B VAL* 1.3 64.4 + - - +
63B GLU* 3.5 8.1 + - - +
64B ALA* 3.5 6.9 + - - +
314B VAL* 3.7 9.2 - - + -
318B GLN* 3.4 26.0 - - - +
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Residues in contact with VAL 61 (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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57B ALA* 4.6 5.6 - - + -
58B SER* 3.2 24.0 + - - +
60B ALA* 1.3 75.8 - - - +
62B LEU* 1.3 67.9 + - + +
64B ALA* 2.8 21.1 + - - +
65B LEU* 3.4 4.6 + - + +
260B ARG 4.5 7.6 - - - +
261B GLY 4.3 2.2 - - - -
262B CYS* 3.9 34.5 - - + +
311B GLY* 3.7 26.3 - - - +
314B VAL* 3.8 17.3 - - + -
315B ALA* 3.8 18.4 - - + +
318B GLN* 4.6 0.7 - - - +
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Residues in contact with LEU 62 (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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66A GLY* 3.8 24.8 - - - +
67A SER 3.9 21.5 - - - +
68A SER* 5.5 2.9 - - - +
70A ASN* 4.0 22.0 - - + +
71A ASN* 5.4 5.8 - - - +
57B ALA* 3.7 33.7 - - + +
58B SER 3.3 9.1 + - - +
59B ARG 3.8 4.7 - - - +
61B VAL* 1.3 79.8 - - + +
63B GLU* 1.3 62.4 + - - +
65B LEU* 2.9 28.2 + - + +
66B GLY 3.8 3.5 + - - -
480B GLY* 4.1 12.1 - - - -
481B LEU* 3.9 22.2 - - + -
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Residues in contact with GLU 63 (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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25A PRO* 3.8 4.6 - - - +
26A LEU* 2.8 39.4 + - + +
27A LYS* 3.9 3.6 + - - +
34A TYR* 5.3 3.3 - - - -
481A LEU* 5.6 0.7 - - - +
484A PHE* 3.3 31.2 - - + -
59B ARG* 2.8 59.9 + - + +
60B ALA 3.6 7.2 - - - +
62B LEU* 1.3 72.2 - - - +
64B ALA* 1.3 58.1 + - - +
66B GLY* 4.1 5.8 + - - -
67B SER 4.5 0.2 + - - -
481B LEU* 4.7 6.2 - - + +
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Residues in contact with ALA 64 (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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26A LEU* 4.2 11.4 - - + -
33A VAL* 5.0 0.2 - - + -
37A ILE* 4.2 17.7 - - + +
484A PHE* 4.6 0.2 - - - -
60B ALA 3.5 7.3 + - - +
61B VAL 2.8 12.6 + - - +
63B GLU* 1.3 76.3 - - - +
65B LEU* 1.3 61.8 + - - +
66B GLY 3.3 0.9 - - - -
67B SER* 2.8 25.8 + - - -
307B HIS* 4.0 8.0 - - - +
310B ALA* 4.2 6.6 - - + +
311B GLY* 4.1 20.2 - - - +
314B VAL* 4.5 6.3 - - + -
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Residues in contact with LEU 65 (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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65A LEU* 3.7 32.5 - - + +
66A GLY* 4.3 0.7 - - - -
70A ASN* 3.4 29.4 - - - +
307A HIS* 4.2 9.0 - - + +
61B VAL 3.4 6.3 + - - +
62B LEU* 2.9 22.7 + - + +
64B ALA* 1.3 79.2 - - - +
66B GLY* 1.3 57.8 + - - +
67B SER 3.2 4.0 + - - +
70B ASN* 4.8 0.2 - - - +
262B CYS* 3.9 22.2 - - + -
307B HIS* 3.5 52.4 - - + +
308B ALA* 3.8 17.0 - - + -
311B GLY* 5.2 0.7 - - - -
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Residues in contact with GLY 66 (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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62A LEU* 3.7 37.2 - - - +
65A LEU* 4.3 3.5 - - - +
66A GLY* 4.6 2.7 - - - +
481A LEU* 3.0 27.6 - - - +
62B LEU 3.8 5.1 + - - -
63B GLU 4.1 5.2 + - - -
64B ALA 3.3 1.0 - - - -
65B LEU* 1.3 78.4 - - - +
67B SER* 1.3 62.1 + - - +
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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