Contacts of the strand formed by residues 37 - 42 (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 PRO 37 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C VAL* 3.5 30.3 - - + -
31C TRP* 6.4 0.4 - - - -
32C PHE* 4.1 16.6 - - + -
35C ASP 4.6 0.7 - - - +
36C VAL* 1.3 91.6 - - + +
38C VAL* 1.3 63.8 + - - +
39C HIS 4.9 0.2 - - - +
40C LEU* 4.5 3.8 - - + -
49C VAL* 3.9 15.0 - - + -
50C VAL 3.5 7.2 - - - +
51C THR* 4.2 1.8 - - - -
353C LEU* 4.0 9.2 - - + +
364C PHE* 3.7 44.1 - - + -
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Residues in contact with VAL 38 (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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36C VAL* 4.0 7.6 - - + +
37C PRO* 1.3 78.4 - - - +
39C HIS* 1.3 64.9 + - + +
50C VAL* 2.8 26.4 + - + +
51C THR 3.6 16.6 - - - +
52C GLY* 3.8 19.7 - - - -
54C ASN* 6.1 1.1 - - - +
90C LYS* 4.9 4.0 - - - +
353C LEU* 3.5 20.9 - - - +
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Residues in contact with HIS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C VAL* 1.3 81.9 + - + +
40C LEU* 1.3 82.7 + - - +
41C SER* 4.5 1.4 - - - -
48C ALA 4.0 0.2 - - - +
49C VAL* 3.6 3.8 - - - -
50C VAL* 2.9 45.4 + - + +
90C LYS 4.2 7.9 - - - +
91C LEU* 3.8 24.4 - - + +
92C ALA* 3.1 40.9 + - + -
144C GLN* 6.1 4.7 - - + -
145C LEU 5.6 5.4 + - - -
299C TYR* 6.0 1.6 - - - -
353C LEU* 3.8 5.0 - - - +
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Residues in contact with LEU 40 (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* 4.8 5.2 - - + -
37C PRO* 4.5 8.3 - - + -
39C HIS* 1.3 93.9 + - - +
41C SER* 1.3 63.1 + - - +
48C ALA 3.6 1.8 - - - +
49C VAL* 3.7 34.8 - - + -
299C TYR* 5.6 2.3 + - - -
353C LEU* 3.6 36.0 - - + +
354C VAL 4.1 4.5 - - - +
355C ALA* 3.7 20.0 - - + +
362C VAL* 3.7 37.7 - - + +
364C PHE* 3.7 16.6 - - + +
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Residues in contact with SER 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C HIS* 4.5 1.3 - - - -
40C LEU* 1.3 75.4 - - - +
42C CYS* 1.3 68.7 + - - +
47C SER* 3.4 3.1 - - - -
48C ALA* 2.8 37.0 + - - +
92C ALA 3.5 22.7 - - - -
93C ALA* 3.3 4.7 - - - +
94C CYS* 2.9 35.9 + - - -
355C ALA* 3.8 3.8 - - - -
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Residues in contact with CYS 42 (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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41C SER* 1.3 82.2 + - - +
43C GLY* 1.3 59.6 + - - +
46C HIS 3.6 3.6 - - - -
47C SER* 3.6 8.3 - - - -
94C CYS* 3.6 11.6 - - - +
355C ALA* 3.5 25.1 - - - +
356C CYS 3.6 15.7 - - - +
357C GLY* 3.6 21.7 - - - +
360C HIS* 3.7 11.4 - - - +
361C MET 4.7 0.2 - - - -
362C VAL* 3.5 32.3 - - - -
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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