Contacts of the strand formed by residues 342 - 348 (chain A) in PDB entry 1SNG
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 PHE 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A PHE* 3.8 19.1 - + - -
223A VAL* 4.2 8.1 - - + -
224A LEU 3.4 15.0 - - - +
225A LEU* 4.0 4.0 - - + -
256A LEU* 4.7 4.9 - - + -
257A PRO* 4.6 9.2 - - + -
259A PHE* 3.8 35.7 - + - -
338A VAL* 3.3 34.5 - - + -
340A ARG 3.5 9.2 - - - +
341A PRO* 1.3 74.3 - - - +
343A HIS* 1.3 82.7 + - - +
344A ILE* 5.0 4.7 - - + -
357A SER* 3.5 1.0 - - - -
358A ILE* 2.9 65.8 + - + -
361A PRO* 4.8 2.2 - - + -
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Residues in contact with HIS 343 (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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20A HIS* 6.0 0.2 - - - +
208A TRP* 3.6 23.2 - + - -
222A ASP 3.8 0.2 - - - +
223A VAL* 3.4 7.1 - - - +
224A LEU* 2.8 46.8 + - + +
226A PRO* 4.2 7.7 - - + +
231A ALA 5.5 0.6 + - - -
232A ALA 5.8 0.4 - - - -
233A ALA 2.9 27.8 + - - -
234A VAL* 4.0 6.7 - - + -
235A PRO* 3.4 27.8 - - + +
341A PRO* 5.1 2.7 + - + +
342A PHE* 1.3 84.7 + - - +
344A ILE* 1.3 61.9 - - - +
345A VAL* 5.7 2.0 - - + -
355A LEU* 6.2 1.3 - - + -
356A GLY 3.1 7.4 - - - +
357A SER* 2.7 33.7 + - - -
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Residues in contact with ILE 344 (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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33A ILE* 5.2 1.8 - - + -
221A VAL* 3.3 36.8 - - + -
222A ASP 3.3 4.7 - - - +
223A VAL* 4.5 8.7 - - + -
256A LEU* 6.3 1.1 - - + -
259A PHE* 3.9 31.2 - - + -
305A LEU* 4.2 20.9 - - + -
307A VAL* 4.0 15.3 - - + -
342A PHE* 4.9 5.1 - - + -
343A HIS* 1.3 76.0 - - - +
345A VAL* 1.3 64.3 + - - +
346A VAL* 4.1 4.7 - - + -
354A PHE 3.8 1.3 - - - +
355A LEU* 3.5 5.8 - - - +
356A GLY* 2.8 52.8 + - - +
358A ILE* 5.0 3.8 - - + -
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Residues in contact with VAL 345 (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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7A PHE* 6.3 0.2 - - + -
8A LEU* 4.8 4.0 - - + -
220A ALA 3.5 1.6 - - - +
221A VAL* 3.4 2.3 - - - -
222A ASP* 2.9 50.8 + - + +
224A LEU* 4.0 22.2 - - + -
235A PRO* 6.2 1.8 - - + -
240A LEU* 4.4 18.2 - - + -
343A HIS* 5.7 2.0 - - + -
344A ILE* 1.3 77.9 - - - +
346A VAL* 1.3 62.0 + - - +
347A ARG* 3.7 12.4 + - + +
352A ILE* 3.9 35.0 - - + -
354A PHE 3.6 2.5 - - - -
355A LEU* 3.8 13.5 - - + -
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Residues in contact with VAL 346 (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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219A LEU* 3.4 40.2 - - + -
220A ALA 3.5 4.7 - - - +
221A VAL* 4.1 19.1 - - + -
305A LEU* 3.8 24.9 - - + -
344A ILE* 4.4 4.0 - - + -
345A VAL* 1.3 72.1 - - - +
347A ARG* 1.3 52.9 + - - +
352A ILE* 3.4 3.7 - - - -
353A LEU* 2.7 34.4 + - + -
354A PHE* 2.9 49.3 + - + +
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Residues in contact with ARG 347 (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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5A GLY 5.4 1.4 + - - -
6A GLY 3.7 20.8 + - - -
7A PHE* 3.7 21.5 - - - +
8A LEU* 3.7 23.8 - - + +
212A THR* 3.9 15.6 + - - +
218A GLU 3.9 0.7 - - - +
219A LEU* 3.7 4.3 - - - +
220A ALA* 2.9 50.3 + - - +
222A ASP* 2.8 40.1 + - - -
244A HIS* 3.9 18.0 + - - -
345A VAL* 4.2 11.2 - - + +
346A VAL* 1.3 75.7 - - - +
348A ARG* 1.3 64.9 + - - +
350A GLY 5.9 0.2 - - - +
351A ALA 3.2 14.1 - - - +
352A ILE* 4.3 1.8 - - - -
353A LEU* 4.2 1.1 - - - +
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Residues in contact with ARG 348 (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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75A ARG 3.4 11.5 + - - -
76A ALA* 2.9 42.2 + - - +
77A VAL* 3.7 4.8 - - - +
78A THR 2.8 29.2 + - - -
79A ASP* 3.3 16.0 + - - +
80A SER* 3.9 13.9 + - - -
217A ASP* 2.7 31.1 + - - +
218A GLU* 3.5 18.3 + - - +
219A LEU* 4.3 6.5 - - + -
347A ARG* 1.3 78.1 - - - +
349A ARG* 1.3 98.2 + - + +
350A GLY 3.3 1.8 - - - -
351A ALA 2.9 17.6 + - - +
353A LEU* 3.8 19.2 - - + +
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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