Contacts of the strand formed by residues 343 - 352 (chain C) in PDB entry 5NXR
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 VAL 343 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C TYR* 3.8 26.2 - - + -
23C PHE 3.6 6.7 - - - +
24C ALA* 4.1 4.5 - - + -
33C GLU* 3.7 31.4 - - + +
114C TRP* 3.5 30.4 - - + -
321C ASP 3.5 2.3 - - - +
322C TYR* 3.4 6.6 - - - -
323C LYS* 2.7 48.0 + - + +
339C ASN* 4.2 2.9 - - - +
341C ASP* 3.9 10.8 - - + +
342C ASN* 1.3 81.4 - - - +
344C LEU* 1.3 61.4 + - - +
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Residues in contact with LEU 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C TYR* 3.4 0.3 - - - -
23C PHE* 2.7 59.8 + - + +
320C VAL* 3.8 28.7 - - + -
321C ASP 3.6 1.1 - - - +
322C TYR* 4.1 20.8 - - + -
343C VAL* 1.3 75.4 - - - +
345C GLY* 1.3 62.7 + - - +
346C LEU* 5.1 5.2 - - + -
402C LDA 3.7 36.6 - - + -
403C LDA 4.1 42.4 + - + -
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Residues in contact with GLY 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C HIS 3.5 6.5 - - - -
22C TYR* 3.8 10.3 - - - -
113C LEU* 3.3 20.6 - - - -
114C TRP* 4.0 3.2 - - - -
320C VAL* 3.3 6.6 - - - +
321C ASP 2.8 35.2 + - - -
343C VAL 4.0 0.8 + - - -
344C LEU* 1.3 74.2 - - - +
346C LEU* 1.3 65.7 + - - +
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Residues in contact with LEU 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ARG* 3.3 5.4 - - - +
21C HIS 2.9 35.0 + - - +
23C PHE* 3.6 31.2 - - + -
113C LEU* 4.2 4.2 - - - +
319C VAL 3.4 3.6 - - - +
320C VAL* 3.7 30.7 - - + -
344C LEU* 5.1 7.4 - - + -
345C GLY* 1.3 82.2 - - - +
347C GLY* 1.3 58.4 + - - +
401C LDA 4.2 30.7 - - + +
402C LDA 5.7 2.2 - - + -
437C LDA 4.8 15.7 - - + +
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Residues in contact with GLY 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ASP* 5.2 1.1 - - - -
19C VAL 3.2 10.8 - - - -
20C ARG* 4.4 6.1 - - - -
113C LEU* 4.8 0.7 - - - -
318C ALA* 3.3 5.2 - - - +
319C VAL* 2.8 50.7 + - - +
346C LEU* 1.3 77.0 - - - +
348C LEU* 1.3 60.6 + - - +
349C VAL* 5.1 0.4 - - - -
401C LDA 4.3 5.6 - - - +
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Residues in contact with LEU 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA* 3.7 12.9 - - + +
83A GLY* 3.7 32.1 - - - +
84A LEU* 5.2 4.9 - - + +
93A ASP* 5.9 0.4 - - - -
94A TYR* 5.4 2.9 - - + +
17C VAL 3.7 1.6 - - - +
19C VAL* 2.9 43.9 + - + +
312C PHE* 4.2 10.3 - - + -
316C MET* 3.7 23.8 - - + -
317C SER 3.5 15.7 - - - +
318C ALA* 3.9 16.2 - - + -
347C GLY* 1.3 74.1 - - - +
349C VAL* 1.3 63.7 + - - +
401C LDA 4.3 12.3 - - + +
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Residues in contact with VAL 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LYS* 4.2 28.3 - - + -
17C VAL 3.3 7.9 - - - +
18C ASP* 3.5 28.3 - - + +
315C ASN 3.8 0.7 - - - +
316C MET* 3.5 9.0 - - - +
317C SER* 2.8 50.2 + - - +
319C VAL* 5.3 11.7 - - + -
347C GLY 5.1 2.0 - - - -
348C LEU* 1.3 79.4 - - - +
350C TYR* 1.3 62.8 + - - +
351C GLN* 3.9 11.5 + - - +
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Residues in contact with TYR 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ASN* 2.7 25.1 + - - -
11A LEU* 4.0 2.4 - - - +
46A GLY* 3.2 43.9 - - - -
47A ASP 3.2 0.7 + - - -
48A THR* 3.7 25.1 - - + -
56A GLY 4.2 0.7 - - - -
57A PHE* 3.9 15.0 - - - +
58A GLY* 3.7 26.7 - - - -
82A ALA* 4.3 6.3 - - + +
16C LYS* 3.3 2.6 - - - +
17C VAL* 2.8 45.3 + - + +
315C ASN 3.5 9.0 - - - -
316C MET* 3.9 15.9 - - - -
348C LEU 4.2 0.8 - - - -
349C VAL* 1.3 71.7 - - - +
351C GLN* 1.3 75.4 + - - +
352C PHE* 4.3 15.3 - + + -
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Residues in contact with GLN 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLY 3.6 11.0 - - - +
16C LYS* 3.9 15.9 - - + +
314C LYS 4.5 9.2 + - - +
315C ASN* 2.7 42.8 + - - +
317C SER* 5.2 5.6 + - - +
349C VAL* 3.9 13.5 + - + +
350C TYR* 1.3 84.0 - - - +
352C PHE* 1.3 69.0 + - - +
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Residues in contact with PHE 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ASN* 4.4 11.4 + - - +
11A LEU* 3.7 42.2 - - + -
44A VAL* 4.3 22.7 - - + -
1C ALA* 3.6 32.1 + - + +
13C VAL* 4.1 21.8 - - + -
14C TYR* 3.5 26.3 - - - +
15C GLY* 2.9 67.0 + - - +
16C LYS* 4.3 3.1 - - - -
17C VAL* 6.0 3.6 - - + -
42C LEU* 4.3 15.0 - - + -
315C ASN* 4.1 7.2 - - - +
350C TYR* 4.3 16.2 - + + -
351C GLN* 1.3 83.5 - - - +
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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