Contacts of the helix formed by residues 49 - 54 (chain C) in PDB entry 1EQB
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 49 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C GLN 3.4 4.2 + - - -
46C ALA 2.8 20.2 + - - -
47C GLN 3.3 1.7 - - - +
48C GLY* 1.3 83.0 - - - +
50C GLN* 1.3 59.8 + - - +
51C LEU* 3.1 32.0 + - - +
52C THR* 3.4 20.1 + - - +
267C HIS* 3.9 2.1 - - - +
19D MET* 3.4 24.8 - - - +
44D MET* 3.8 4.2 - - - +
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Residues in contact with GLN 50 (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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4C ARG* 2.6 36.4 + - - +
49C SER* 1.3 71.4 - - - +
51C LEU* 1.3 59.1 + - + +
52C THR* 2.9 11.8 + - - -
53C ASN* 3.0 13.8 + - - +
22D GLU* 5.7 0.4 - - + -
23D LYS* 3.7 32.1 + - + +
26D GLN* 2.8 49.3 + - - +
27D GLU* 5.8 0.8 + - - +
44D MET* 4.1 15.5 - - - -
416D TYR* 3.2 29.9 - - + -
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Residues in contact with LEU 51 (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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49C SER* 3.1 18.9 - - - +
50C GLN* 1.3 78.6 - - + +
52C THR* 1.3 58.9 + - - +
53C ASN 3.1 2.5 + - - -
54C LYS* 3.5 14.9 + - - +
70C TYR 6.3 0.2 - - - -
71C VAL* 4.8 7.9 - - + -
74C VAL* 4.2 15.5 - - + -
266C MET* 3.7 29.2 + - + +
267C HIS* 3.7 15.0 + - - +
270C ALA* 3.7 30.3 - - + -
19D MET* 4.2 23.3 - - + +
22D GLU* 3.3 36.8 - - + -
26D GLN* 4.7 1.8 - - - +
235D ARG* 5.4 0.2 - - - -
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Residues in contact with THR 52 (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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49C SER 3.4 18.2 + - - +
50C GLN* 2.9 3.1 - - - -
51C LEU* 1.3 79.4 - - - +
53C ASN* 1.3 61.1 + - - +
54C LYS 3.5 0.2 - - - -
267C HIS* 3.5 28.4 + - - +
39D THR* 3.8 27.5 - - + +
44D MET* 4.2 4.5 - - + -
47D GLN* 3.4 28.8 + - - +
228D HIS* 5.6 0.7 - - - +
234D PRO* 4.6 3.6 - - - +
235D ARG* 2.9 36.6 + - - +
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Residues in contact with ASN 53 (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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50C GLN* 3.0 16.8 + - - +
52C THR* 1.3 82.9 - - - +
54C LYS* 1.3 58.2 + - - +
26D GLN* 3.1 29.5 + - - +
36D GLU* 3.3 25.3 - - - +
37D ASN 3.4 22.6 + - - +
38D TYR* 4.0 6.5 - - + -
39D THR* 3.1 31.2 + - - +
44D MET* 5.3 0.2 - - - -
235D ARG* 3.9 4.1 + - - +
416D TYR* 3.1 25.8 + - - -
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Residues in contact with LYS 54 (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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50C GLN 4.4 0.4 + - - -
51C LEU* 3.5 14.3 + - - +
53C ASN* 1.3 77.7 - - - +
55C TYR* 1.3 89.1 + - - +
56C ALA* 3.8 2.9 + - + -
65C PHE* 3.7 4.6 - - - +
66C GLY 2.7 29.8 + - - -
67C GLY 3.5 16.4 - - - +
68C CYS* 3.7 8.8 - - - -
71C VAL* 4.0 24.7 - - + -
264C PRO 4.8 2.4 - - - +
266C MET* 4.3 10.1 + - + +
22D GLU* 3.8 8.1 - - - +
25D ARG* 3.6 31.4 - - - +
26D GLN* 4.7 1.7 - - - +
31D GLU* 4.4 0.9 - - - -
33D ILE* 3.7 8.3 - - - +
36D GLU* 3.2 16.8 + - - +
235D ARG* 3.5 15.7 + - - -
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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