Contacts of the strand formed by residues 271 - 279 (chain A) in PDB entry 6ZGI
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 GLN 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LEU* 4.1 4.5 - - - -
55A PHE 2.9 33.2 + - - +
57A PRO* 4.1 15.3 - - + +
269A TYR* 4.0 8.3 + - + +
270A LEU* 1.3 78.2 - - - +
272A PRO* 1.3 74.7 - - + +
273A ARG* 3.3 31.8 + - + +
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Residues in contact with PRO 272 (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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52A GLN* 4.0 20.0 + - - +
53A ASP 3.5 7.2 - - - +
54A LEU* 4.0 22.2 - - + -
88A ASP* 5.2 8.7 - - - +
270A LEU 4.9 0.4 - - - +
271A GLN* 1.3 86.8 - - + +
273A ARG* 1.3 68.5 + - - +
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Residues in contact with ARG 273 (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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52A GLN* 3.4 5.2 - - - +
53A ASP 2.9 33.2 + - - +
55A PHE* 3.8 13.0 - - + +
57A PRO* 3.6 28.5 - - + +
271A GLN* 3.5 33.4 - - + +
272A PRO* 1.3 83.1 - - - +
274A THR* 1.3 62.9 + - - +
275A PHE* 3.9 22.7 - - + -
290A ASP* 3.4 29.9 + - - +
292A ALA* 3.8 32.4 + - - +
293A LEU* 4.1 4.2 - - - +
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Residues in contact with THR 274 (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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50A SER* 4.9 8.3 - - - -
51A THR 3.5 16.6 - - - +
52A GLN* 3.3 21.7 - - + +
273A ARG* 1.3 71.0 - - - +
275A PHE* 1.3 77.1 + - - +
290A ASP* 4.0 1.4 - - - +
291A CYS* 3.2 38.0 + - + +
292A ALA* 4.8 2.7 + - - +
301A CYS* 4.9 3.1 - - - -
754B LEU* 5.0 10.6 - - + +
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Residues in contact with PHE 275 (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 6.0 0.2 - - - -
36A VAL* 4.1 16.8 - - + -
49A HIS 3.9 0.7 - - - +
50A SER* 3.4 3.9 - - - -
51A THR 2.9 32.2 + - - +
55A PHE* 3.8 43.1 - + + -
56A LEU 3.9 15.7 - - - -
58A PHE* 3.6 28.0 - + - -
273A ARG* 3.9 15.0 - - + -
274A THR* 1.3 83.6 - - - +
276A LEU* 1.3 60.1 + - - +
277A LEU* 3.7 18.0 - - + +
288A ALA* 4.4 11.7 - - + -
289A VAL 3.4 5.2 - - - -
290A ASP* 3.4 35.7 - - + -
291A CYS* 4.4 3.1 - - - -
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Residues in contact with LEU 276 (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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48A LEU* 4.3 12.1 - - + -
49A HIS 3.6 18.6 - - - +
50A SER* 3.2 23.3 - - - +
275A PHE* 1.3 71.2 - - - +
277A LEU* 1.3 62.3 + - - +
288A ALA* 3.2 4.4 - - - -
289A VAL* 2.9 51.0 + - + +
291A CYS* 4.1 10.5 - - - -
300A LYS 4.2 18.8 - - - +
301A CYS* 4.4 9.2 - - - +
304A LYS* 4.3 24.2 - - + +
305A SER 4.5 4.7 - - - +
306A PHE* 4.2 21.1 - - + -
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Residues in contact with LEU 277 (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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36A VAL* 3.8 17.5 - - + -
37A TYR 5.4 1.1 - - - +
39A PRO* 5.4 5.8 - - + -
47A VAL 3.9 0.7 - - - +
48A LEU* 3.4 6.1 - - - +
49A HIS* 2.9 37.8 + - + +
51A THR* 3.4 33.2 - - + -
55A PHE* 4.8 4.9 - - + -
275A PHE* 3.7 20.0 - - + +
276A LEU* 1.3 74.6 - - - +
278A LYS* 1.3 59.7 + - - +
279A TYR* 4.3 17.7 - - + +
285A ILE* 3.7 29.2 - - + -
287A ASP 3.7 1.1 - - - -
288A ALA* 3.6 24.2 - - + -
306A PHE* 5.2 0.2 - - - -
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Residues in contact with LYS 278 (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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47A VAL 3.7 2.9 - - - -
48A LEU* 3.7 25.6 - - + +
277A LEU* 1.3 73.9 - - - +
279A TYR* 1.3 70.6 + - - +
280A ASN* 6.1 2.7 - - - +
285A ILE* 3.2 6.9 - - - -
286A THR* 3.1 41.2 + - - +
287A ASP* 2.9 31.1 + - + +
306A PHE* 4.0 21.3 - - + +
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Residues in contact with TYR 279 (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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38A TYR* 4.6 8.1 - + - -
39A PRO* 4.3 16.1 - - - +
40A ASP* 6.1 0.7 - - - -
42A VAL 5.5 3.4 + - - -
44A ARG* 3.6 48.8 + - + +
46A SER* 3.0 8.4 - - - +
47A VAL* 2.9 54.0 + - + +
49A HIS* 3.9 24.3 + - + -
277A LEU* 4.3 15.5 - - + +
278A LYS* 1.3 81.0 - - - +
280A ASN* 1.3 60.3 + - - +
283A GLY 3.9 15.9 - - - -
284A THR 3.6 2.9 - - - +
285A ILE* 3.7 30.9 - - + +
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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