Contacts of the strand formed by residues 270 - 275 (chain A) in PDB entry 1QS0
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 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A VAL* 4.6 7.2 - - + -
44A ALA* 3.7 13.3 - - - +
47A THR* 3.8 10.8 - - + +
269A ILE* 1.3 73.7 - - - +
271A SER* 1.3 58.9 + - - +
288A TRP* 4.5 13.5 - - + -
292A ARG* 3.5 43.1 - - - +
299A PRO 4.3 2.7 + - - +
300A SER* 3.4 4.5 - - - -
301A LEU 2.9 23.7 + - - -
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Residues in contact with SER 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 2.5 36.8 + - - +
50A LEU* 4.1 2.4 - - - +
51A SER* 4.3 2.0 + - - -
261A ALA* 3.1 34.3 + - - -
264A GLY* 3.2 12.3 - - - -
265A VAL* 3.3 11.2 + - - -
269A ILE 3.0 14.6 + - - -
270A ALA* 1.3 71.5 - - - +
272A LEU* 1.3 69.6 + - - +
288A TRP* 6.1 0.2 - - - -
301A LEU* 3.1 13.9 - - - +
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Residues in contact with LEU 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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38A PRO* 4.9 3.4 - - + -
47A THR* 4.2 2.2 - - - +
50A LEU* 4.1 27.4 - - + -
55A VAL* 4.5 6.7 - - + -
68A TRP* 3.9 24.9 - - + -
261A ALA* 3.9 4.7 - - - +
271A SER* 1.3 86.9 - - - +
273A ARG* 1.3 54.7 + - - +
274A VAL* 3.8 11.0 - - + -
285A ALA* 4.4 15.5 - - + +
288A TRP* 3.5 39.3 - - + -
301A LEU 2.8 11.3 + - - +
302A ILE* 3.2 15.6 - - + +
303A GLU 2.7 32.9 + - - +
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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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26A TYR 5.3 0.2 + - - -
27A LEU* 4.3 10.1 - - - +
28A ARG* 2.7 56.6 + - - +
29A LEU* 4.8 1.2 - - - +
50A LEU* 3.8 16.3 + - - +
51A SER 3.7 17.5 - - - +
53A SER* 3.1 24.7 + - - +
54A LEU* 3.2 10.3 + - + +
55A VAL* 2.8 32.5 + - - +
241A ASN* 5.1 3.0 - - - +
259A THR* 4.0 13.1 - - - +
261A ALA* 4.1 2.9 - - + -
272A LEU* 1.3 71.2 - - - +
274A VAL* 1.3 53.5 + - - +
303A GLU* 3.4 32.4 + - - +
305A VAL* 3.6 35.3 - - + +
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Residues in contact with VAL 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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54A LEU* 3.5 5.8 - - - -
55A VAL* 3.4 25.4 - - + +
272A LEU* 4.2 9.9 - - + -
273A ARG* 1.3 77.0 - - - +
275A ASP* 1.3 76.4 + - - +
276A GLY 3.0 0.7 + - - -
281A ALA* 3.7 20.2 - - + +
285A ALA* 3.6 22.7 - - + -
302A ILE* 4.0 14.8 - - + -
303A GLU 2.9 9.9 + - - +
304A TRP* 3.6 23.4 - - + -
305A VAL* 2.9 27.7 + - - +
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Residues in contact with ASP 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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54A LEU* 3.4 13.7 - - + +
55A VAL 2.9 18.7 + - - +
56A ARG* 3.6 14.2 - - + -
274A VAL* 1.3 78.8 - - - +
276A GLY* 1.3 60.9 + - - +
277A ASN* 2.6 35.2 + - - +
278A ASP* 3.0 29.5 + - + +
282A VAL* 3.7 6.4 - - - +
305A VAL 4.2 2.7 - - - -
332A LEU* 3.0 32.0 - - - +
338A ARG* 3.0 18.4 + - - -
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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