Contacts of the strand formed by residues 47 - 53 (chain C) in PDB entry 6H25
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 GLY 47 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C ALA* 3.3 3.6 - - - +
46C ASP* 1.3 82.5 - - - +
48C SER* 1.3 62.0 + - - -
60C CYS 4.0 0.3 - - - +
61C GLY* 3.5 3.1 - - - -
62C VAL* 2.9 35.5 + - - +
159C ALA* 4.1 12.6 - - - -
162C ASN* 3.4 19.3 - - - -
163C VAL* 4.5 1.1 - - - -
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Residues in contact with SER 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ILE* 4.3 1.9 - - - +
40C GLY* 3.3 21.5 + - - -
41C SER* 3.1 10.9 + - - -
42C ILE* 3.1 55.4 + - - -
45C ALA* 5.1 2.7 - - - -
47C GLY* 1.3 74.4 - - - -
49C ALA* 1.3 61.8 + - - +
60C CYS 3.4 7.2 - - - -
61C GLY* 5.2 2.0 - - - -
158C ALA 4.7 0.9 - - - +
159C ALA* 4.4 2.6 - - - -
162C ASN* 3.1 14.4 + - - +
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Residues in contact with ALA 49 (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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38C ASN 3.6 6.5 - - - +
39C ILE* 5.0 0.4 - - + -
41C SER* 6.5 0.2 - - - -
42C ILE* 6.3 0.7 - - - -
48C SER* 1.3 76.6 - - - +
50C LEU* 1.3 62.1 + - - +
51C VAL 4.2 0.2 - - - -
58C VAL 3.9 0.5 - - - +
59C ILE* 3.3 8.0 - - - +
60C CYS 2.9 31.5 + - - +
155C ALA* 3.4 31.2 - - - +
158C ALA* 3.7 15.0 - - + -
159C ALA* 3.5 15.3 - - + +
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Residues in contact with LEU 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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36C THR 4.0 0.2 - - - +
37C VAL* 3.1 7.3 - - - +
38C ASN* 2.9 67.3 + - + +
41C SER* 5.2 8.9 - - - +
49C ALA* 1.3 74.3 - - - +
51C VAL* 1.3 67.6 + - - +
52C LYS* 4.5 16.4 - - + -
57C THR* 3.7 25.6 - - + -
58C VAL 3.7 0.7 - - - +
59C ILE* 3.7 28.0 - - + -
142C LEU* 5.0 0.9 - - + -
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Residues in contact with VAL 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C THR* 5.9 0.9 - - - -
36C THR 3.6 6.7 - - - +
37C VAL* 3.7 16.4 - - + -
49C ALA* 5.2 2.0 - - + -
50C LEU* 1.3 81.1 - - - +
52C LYS* 1.3 64.9 + - - +
53C LEU* 4.0 23.3 - - + +
56C THR 3.5 1.4 - - - +
57C THR* 3.3 4.9 - - - +
58C VAL* 2.9 38.6 + - + +
151C ALA* 4.4 11.2 - - + +
154C PHE* 3.9 20.6 - - + +
155C ALA* 3.7 35.4 - - + +
158C ALA* 5.3 1.1 - - + -
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Residues in contact with LYS 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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34C THR 3.7 2.1 - - - +
35C THR* 3.5 1.2 - - - -
36C THR* 2.9 53.5 + - - +
38C ASN* 5.6 3.4 - - - +
50C LEU* 4.2 18.1 - - + -
51C VAL* 1.3 76.8 - - - +
53C LEU* 1.3 60.5 + - - +
54C GLY 4.2 0.4 - - - -
55C ASN* 5.4 7.5 - - - +
56C THR 3.4 5.6 - - - +
57C THR* 3.4 31.8 + - + +
45F LEU* 4.5 17.6 + - - +
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Residues in contact with LEU 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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32C PHE* 5.5 2.0 - - + -
33C ARG* 5.3 1.8 - - + +
34C THR 3.3 4.0 - - - +
35C THR* 3.7 26.9 - - + -
51C VAL* 4.0 11.7 - - + -
52C LYS* 1.3 75.3 - - - +
54C GLY* 1.3 61.5 + - - +
55C ASN 3.4 0.4 - - - -
56C THR* 2.3 56.0 + - + +
146C GLY 4.9 6.3 - - - +
147C ASN* 4.9 4.5 - - + +
150C ASP* 4.5 17.0 - - - +
151C ALA* 3.8 33.4 - - + +
154C PHE* 5.1 5.2 - - + -
209C ASP* 4.0 26.5 - - - +
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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