Contacts of the strand formed by residues 13 - 18 (chain C) in PDB entry 4JHN
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 ALA 13 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C MET* 3.8 5.8 - - - -
12C GLY* 1.3 75.6 - - - +
14C VAL* 1.3 60.8 + - - +
15C PHE* 3.5 9.6 - - + -
29C LYS* 3.7 35.0 - - + -
30C PHE 3.6 11.9 - - - +
31C TRP* 3.9 9.6 - - + -
364C PHE* 3.3 10.5 - - - -
365C ALA 3.0 31.6 + - - +
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Residues in contact with VAL 14 (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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13C ALA* 1.3 73.5 - - - +
15C PHE* 1.3 65.5 + - - +
29C LYS* 3.2 5.9 - - - +
30C PHE* 2.8 81.5 + - + +
31C TRP* 5.5 0.7 - - - -
32C PHE* 4.6 2.9 - - + -
37C PRO* 3.5 33.7 - - + -
40C LEU* 4.8 4.5 - - + -
49C VAL* 4.9 3.6 - - + -
362C VAL* 3.4 29.6 - - + -
363C VAL 3.2 6.5 - - - +
364C PHE* 4.4 4.3 - - + -
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Residues in contact with PHE 15 (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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13C ALA* 3.5 25.8 - - + -
14C VAL* 1.3 72.8 - - - +
16C THR* 1.3 63.4 + - - +
17C PHE* 3.9 11.4 - + + -
28C GLY 3.4 8.5 - - - +
29C LYS* 3.8 40.8 - - + -
346C PHE* 3.6 41.3 - + + -
349C PHE* 3.9 25.1 - + - -
361C MET 3.9 0.5 - - - +
362C VAL* 3.5 3.6 - - - +
363C VAL* 2.7 45.3 + - + +
365C ALA* 4.1 15.0 - - + -
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Residues in contact with THR 16 (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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14C VAL* 4.6 1.1 - - + -
15C PHE* 1.3 75.5 - - - +
17C PHE* 1.3 69.6 + - - +
20C SER* 3.5 20.7 + - - +
22C PHE* 3.4 14.4 + - + +
26C ASN 4.7 1.2 + - - -
27C PRO* 3.3 7.3 - - - +
28C GLY* 2.9 45.9 + - - +
30C PHE* 3.9 27.4 - - + -
59C PHE* 4.1 16.6 - - + -
361C MET 3.5 4.7 - - - -
362C VAL* 4.3 8.7 - - + -
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Residues in contact with PHE 17 (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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15C PHE* 3.9 21.5 - + + -
16C THR* 1.3 80.1 - - - +
18C GLY* 1.3 62.4 + - - +
20C SER* 4.3 2.9 - - - -
25C ASN* 5.5 0.7 - - - +
26C ASN 5.8 0.2 - - - -
27C PRO* 4.2 27.1 - - + -
28C GLY 6.0 0.2 - - - -
325C GLY 3.5 15.3 - - - +
326C LYS* 4.2 10.8 - - - +
328C GLY* 3.6 20.6 - - - -
345C ASN* 3.9 13.2 - - - -
346C PHE* 3.7 38.8 - + - -
360C HIS* 3.2 8.4 - - - +
361C MET* 2.9 53.0 + - + +
363C VAL* 3.9 7.9 - - + -
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Residues in contact with GLY 18 (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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17C PHE* 1.3 77.5 - - - +
19C LYS* 1.3 59.9 + - - -
20C SER* 3.1 8.1 + - - -
22C PHE 5.5 1.4 - - - +
25C ASN* 2.8 34.9 + - - +
26C ASN 5.2 1.4 - - - +
324C HIS* 3.3 24.1 + - - -
325C GLY 4.0 2.4 + - - -
326C LYS* 4.1 4.0 - - - -
359C CYS 3.3 9.6 - - - -
360C HIS* 4.1 0.7 - - - -
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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