Contacts of the strand formed by residues 351 - 362 (chain A) in PDB entry 1NQG
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 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A GLN* 3.8 1.6 - - - +
348A VAL* 2.8 38.8 + - + +
349A GLY 4.1 1.4 - - - +
350A ASP* 1.3 90.6 - - + +
352A THR* 1.3 65.0 + - - +
353A PHE* 3.5 30.3 - + + -
375A ALA* 5.7 2.7 - - + -
376A GLY 3.0 14.1 - - - -
377A TRP* 3.5 43.7 - + + -
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Residues in contact with THR 352 (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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21A THR* 4.9 7.0 - - - +
23A LEU* 3.7 33.4 - - + -
345A LEU* 4.3 12.6 - - + -
346A GLN 3.8 8.5 - - - +
347A GLN* 3.9 15.7 + - + +
350A ASP 5.2 0.7 + - - -
351A PHE* 1.3 76.9 + - - +
353A PHE* 1.3 79.2 + - - +
354A GLU* 5.2 0.2 - - + -
375A ALA* 3.2 5.0 - - - +
376A GLY* 2.6 32.1 + - - -
384A ARG* 4.0 14.0 + - - +
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Residues in contact with PHE 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 3.3 5.2 - - - +
346A GLN* 2.9 40.8 + - + +
348A VAL* 3.6 22.0 - - + -
351A PHE* 3.5 38.8 - + + -
352A THR* 1.3 78.7 - - - +
354A GLU* 1.3 62.2 + - - +
373A THR* 6.0 0.9 - - + -
374A SER 3.5 5.6 - - - +
375A ALA* 3.8 20.4 - - + -
803A C8E 3.2 39.7 + - - +
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Residues in contact with GLU 354 (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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12A ALA* 4.5 7.4 - - - +
13A ASN* 6.1 0.9 - - - +
17A GLN* 4.3 9.4 + - - +
21A THR 3.7 10.4 - - - +
22A VAL* 4.2 12.0 - - - +
23A LEU* 3.1 39.0 + - + +
114A ARG* 4.0 21.3 + - - +
344A GLY 3.1 11.4 - - - +
345A LEU* 4.8 9.2 - - + -
353A PHE* 1.3 78.0 - - - +
355A GLY* 1.3 65.5 + - - +
373A THR* 3.6 5.7 - - - +
374A SER* 3.0 33.3 + - - +
803A C8E 4.1 4.2 - - - +
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Residues in contact with GLY 355 (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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343A THR* 3.5 2.4 - - - -
344A GLY 2.8 30.8 + - - +
354A GLU* 1.3 82.0 - - - +
356A ALA* 1.3 63.1 - - - +
372A GLN* 3.4 14.4 - - - -
373A THR* 4.4 0.9 - - - -
803A C8E 3.5 19.5 - - - -
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Residues in contact with ALA 356 (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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116A ALA* 3.5 22.4 - - + +
117A VAL* 3.6 20.9 - - + -
342A LEU 3.1 13.2 - - - +
343A THR* 4.0 3.4 - - + -
355A GLY* 1.3 74.9 - - - +
357A ALA* 1.3 63.5 + - - +
371A TRP* 3.5 2.4 - - - +
372A GLN* 3.2 38.0 + - + +
803A C8E 3.4 6.7 - - - +
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Residues in contact with ALA 357 (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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116A ALA* 3.6 1.8 - - - -
341A TYR* 3.1 4.5 - - - +
342A LEU* 2.8 34.9 + - + +
356A ALA* 1.3 76.3 - - - +
358A ARG* 1.3 60.7 + - - +
370A THR 3.2 9.6 - - - +
371A TRP* 4.2 4.5 - - + -
800A C8E 3.3 20.5 - - + +
803A C8E 4.6 1.6 - - + -
805A C8E 3.1 35.7 - - + -
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Residues in contact with ARG 358 (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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14A ARG* 3.8 1.4 - - - +
84A ARG* 5.9 1.6 - - - +
115A SER 3.0 17.9 - - - -
116A ALA* 3.5 16.8 + - - +
117A VAL 2.8 33.6 + - - -
118A TYR 3.3 6.3 + - - -
119A GLY* 3.3 13.4 - - - +
316A ASP* 3.0 36.9 + - - +
337A ASN* 4.4 4.0 + - - -
339A GLY* 4.0 14.5 - - - +
340A ILE 3.5 5.8 - - - +
341A TYR* 3.9 12.5 - - + -
357A ALA* 1.3 75.3 - - - +
359A SER* 1.3 63.6 + - - +
360A ASP* 3.0 36.8 + - - +
369A GLY* 4.3 0.2 - - - -
370A THR* 2.7 21.6 + - + -
800A C8E 2.2 37.2 - - - +
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Residues in contact with SER 359 (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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338A THR 4.0 0.6 - - - +
339A GLY* 2.9 2.6 - - - -
340A ILE* 2.6 54.2 + - - +
358A ARG* 1.3 75.2 + - - +
360A ASP* 1.3 61.4 + - - +
367A ARG* 2.7 39.7 + - - -
368A HIS 3.9 6.5 + - - -
369A GLY* 4.1 3.3 - - - -
800A C8E 3.8 11.4 - - - +
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Residues in contact with ASP 360 (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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115A SER 4.6 0.3 - - - +
119A GLY* 3.9 0.9 - - - -
337A ASN* 3.0 20.3 - - - +
338A THR 3.4 2.7 - - - -
339A GLY* 3.7 1.7 - - - -
358A ARG* 3.0 48.3 + - - +
359A SER* 1.3 75.7 - - - +
361A ASP* 1.3 59.0 + - - +
362A ASN 3.9 0.7 - - - +
365A PHE* 5.4 2.0 - - + -
366A GLY 3.4 1.4 - - - +
367A ARG* 3.2 5.6 - - - +
368A HIS* 2.9 39.2 + - + +
370A THR* 5.5 2.1 - - - +
393A TYR* 3.5 36.6 + - + +
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Residues in contact with ASP 361 (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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336A ARG 4.1 0.3 - - - +
337A ASN* 3.4 5.0 + - - -
338A THR* 2.6 40.8 + - - +
360A ASP* 1.3 72.4 - - - +
362A ASN* 1.3 62.4 + - - +
363A SER 4.0 0.5 + - - -
366A GLY* 3.4 18.3 - - - -
367A ARG* 3.9 8.6 + - - +
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Residues in contact with ASN 362 (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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335A GLN* 5.4 7.3 + - - +
336A ARG 4.0 4.8 - - - +
337A ASN* 3.1 20.4 + - - +
360A ASP 3.9 0.4 - - - -
361A ASP* 1.3 74.4 - - - +
363A SER* 1.3 58.2 + - - +
364A GLN* 2.6 51.0 + - - +
365A PHE* 2.8 54.5 - - + +
366A GLY* 2.4 35.3 + - - +
395A ALA* 5.2 4.0 - - - +
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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