Contacts of the strand formed by residues 48 - 55 (chain A) in PDB entry 7CN9
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 LEU 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A VAL* 1.3 82.0 - - - +
49A HIS* 1.3 73.0 + - - +
276A LEU* 3.6 27.8 - - + -
277A LEU 3.3 15.7 - - - +
278A LYS* 3.5 25.4 - - + -
279A TYR* 5.5 0.7 - - - -
304A LYS* 3.1 53.8 - - + +
305A SER* 4.0 2.5 - - - +
306A PHE* 3.8 6.7 - - + -
567C ARG* 4.5 1.0 + - - -
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Residues in contact with HIS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG* 4.6 24.5 - - - +
48A LEU* 1.3 81.7 + - - +
50A SER* 1.3 77.9 + - - +
51A THR* 5.3 5.2 - - + +
276A LEU* 4.7 3.1 - - - -
277A LEU* 2.9 38.0 + - - +
279A TYR* 5.0 1.5 - - + -
964A LYS* 5.0 19.3 - - + -
567C ARG* 3.3 28.3 + - - +
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Residues in contact with SER 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A HIS* 1.3 88.4 + - - +
51A THR* 1.3 81.3 + - - +
274A THR* 3.1 8.0 + - - -
275A PHE 2.5 23.9 + - - -
276A LEU* 4.1 15.7 - - - -
301A CYS* 5.7 5.4 - - - -
304A LYS* 5.8 4.5 - - - -
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Residues in contact with THR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A PRO* 4.2 27.2 - - + +
44A ARG* 5.4 4.9 - - - +
49A HIS* 5.3 6.3 - - + -
50A SER* 1.3 83.9 + - - +
52A GLN* 1.3 64.1 + - - +
53A ASP* 4.3 2.9 + - - +
55A PHE* 3.8 21.5 - - - -
274A THR* 2.2 30.1 + - - -
275A PHE* 2.9 14.5 + - - +
277A LEU* 6.2 1.3 - - + +
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Residues in contact with GLN 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A THR* 1.3 84.6 + - - +
53A ASP* 1.3 63.2 + - - +
272A PRO* 5.6 8.5 - - - +
273A ARG 4.2 0.9 - - - -
274A THR* 3.4 28.7 - - - +
275A PHE 4.4 0.2 - - - +
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Residues in contact with ASP 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A TYR* 2.7 22.6 + - + +
39A PRO 5.1 2.8 - - - +
51A THR* 4.9 5.2 - - - +
52A GLN* 1.3 76.9 - - - +
54A LEU* 1.3 88.0 + - - +
55A PHE* 2.7 40.6 + - + +
195A LYS* 2.7 19.1 + - - -
197A ILE* 5.8 1.6 - - - +
271A GLN 3.6 5.2 - - - +
272A PRO* 4.1 8.1 - - - +
273A ARG 3.6 6.6 + - - +
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A TYR* 3.1 27.4 + - - -
53A ASP* 1.3 100.8 + - - +
55A PHE* 1.3 57.9 + - - +
88A ASP* 3.2 43.3 - - + +
89A GLY* 3.6 8.1 - - - +
195A LYS* 3.3 30.3 - - + +
196A ASN* 5.1 10.3 - - - +
270A LEU* 3.5 9.1 - - + +
271A GLN 3.5 10.5 - - - -
272A PRO* 4.6 5.9 - - + +
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Residues in contact with PHE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLY 3.9 11.0 - - - -
36A VAL* 4.0 8.5 - - + -
37A TYR* 3.7 44.9 - + - -
39A PRO* 5.9 4.0 - - + -
51A THR* 3.8 18.4 - - - -
53A ASP* 2.7 27.7 + - + +
54A LEU* 1.3 73.1 - - - +
56A LEU* 1.3 57.3 + - - +
57A PRO* 3.5 3.4 - - - +
270A LEU* 3.0 9.2 - - - +
271A GLN 2.7 31.9 + - - +
273A ARG 3.9 5.8 - - - +
275A PHE* 3.2 67.8 - + + -
277A LEU* 5.0 6.7 - - + -
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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