Contacts of the strand formed by residues 13 - 18 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D MET* 3.8 14.8 - - + -
12D GLY* 1.3 75.3 - - - +
14D VAL* 1.3 60.1 + - - +
15D PHE* 3.4 11.6 - - + -
29D LYS* 3.9 16.6 - - + -
30D PHE 3.6 12.1 - - - +
31D TRP* 3.8 20.0 - - + +
364D PHE* 3.3 10.2 - - - -
365D ALA 3.1 30.3 + - - +
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Residues in contact with VAL 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ALA* 1.3 72.8 - - - +
15D PHE* 1.3 62.3 + - - +
16D THR 4.2 0.2 + - - -
29D LYS* 3.3 5.0 - - - -
30D PHE* 2.8 77.3 + - + +
31D TRP* 5.6 0.2 - - - -
32D PHE* 4.7 2.5 - - + -
37D PRO* 3.5 33.9 - - + -
40D LEU* 4.1 8.1 - - + -
49D VAL* 4.9 1.3 - - + -
362D VAL* 3.3 34.1 - - + -
363D VAL 3.3 6.1 - - - +
364D PHE* 4.3 6.1 - - + -
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Residues in contact with PHE 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ALA* 3.4 25.8 - - + -
14D VAL* 1.3 72.2 - - - +
16D THR* 1.3 61.6 + - - +
17D PHE* 3.9 9.9 - + + -
28D GLY 3.3 9.6 - - - +
29D LYS* 3.8 40.8 - - + -
346D PHE* 3.6 31.0 - + + -
349D PHE* 3.9 24.2 - + - -
361D MET 3.9 0.3 - - - +
362D VAL* 3.4 4.5 - - - +
363D VAL* 2.7 54.6 + - + +
365D ALA* 4.0 15.7 - - + -
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Residues in contact with THR 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D PHE* 1.3 75.9 - - - +
17D PHE* 1.3 67.9 + - - +
20D SER* 3.5 22.9 + - - +
22D PHE* 3.4 13.0 - - + +
26D ASN 4.5 1.2 + - - -
27D PRO* 3.3 7.4 - - - +
28D GLY* 2.9 46.2 + - - +
30D PHE* 3.9 27.4 - - + -
59D PHE* 4.1 16.6 - - + -
361D MET 3.6 3.1 - - - -
362D VAL* 4.2 10.3 - - + -
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Residues in contact with PHE 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PHE* 3.9 12.8 - + + -
16D THR* 1.3 78.9 - - - +
18D GLY* 1.3 62.2 + - - +
20D SER* 4.5 2.5 - - - -
26D ASN 5.4 0.4 - - - -
27D PRO* 4.2 26.9 - - + -
325D GLY 3.5 15.5 - - - +
326D LYS* 4.1 11.2 - - - +
328D GLY* 3.6 20.4 - - - -
330D GLY* 5.6 4.0 - - - -
345D ASN* 3.9 11.7 - - - -
346D PHE* 3.8 25.1 - + - -
360D HIS* 3.2 8.5 - - - +
361D MET* 2.9 52.3 + - + +
363D VAL* 3.5 28.9 - - + -
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Residues in contact with GLY 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PHE* 1.3 76.1 - - - +
19D LYS* 1.3 62.7 + - - +
20D SER* 3.3 7.5 + - - -
22D PHE 6.1 0.3 - - - -
26D ASN* 4.7 19.5 + - - +
27D PRO* 5.8 0.4 - - - +
324D HIS* 3.3 31.5 + - - +
325D GLY 4.1 0.8 + - - -
326D LYS* 4.0 5.6 - - - +
359D CYS 3.3 10.1 - - - -
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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