Contacts of the strand formed by residues 316 - 325 (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 MET 316 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A THR* 4.0 9.2 - - + -
50A ILE* 4.5 0.9 - - + -
56A GLY* 4.0 7.9 - - - -
57A PHE 4.3 0.7 - - - +
82A ALA* 4.8 0.9 - - + -
83A GLY 3.2 31.2 - - - +
84A LEU* 3.9 13.2 - - + -
312C PHE* 3.0 46.5 + - + -
313C ASN* 3.0 19.9 + - - +
314C LYS 3.6 0.4 - - - -
315C ASN* 1.3 78.2 - - - +
317C SER* 1.3 62.5 + - - +
348C LEU* 3.7 36.6 - - + -
349C VAL 3.5 10.1 - - - +
350C TYR* 3.9 26.7 - - - -
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Residues in contact with SER 317 (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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309C TYR* 5.5 5.2 - - - -
310C TYR 3.2 12.6 - - - -
311C TYR* 4.0 24.6 - - - -
312C PHE* 3.9 5.4 - - - -
313C ASN 5.3 0.2 - - - -
315C ASN 5.7 0.3 - - - -
316C MET* 1.3 76.7 - - - +
318C ALA* 1.3 64.8 + - - +
319C VAL* 5.5 2.0 - - - +
348C LEU* 3.5 5.9 - - - +
349C VAL* 2.8 48.3 + - - +
351C GLN* 5.2 5.9 + - - +
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Residues in contact with ALA 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C TYR* 4.3 0.2 - - - +
310C TYR* 2.7 41.5 + - + +
312C PHE* 3.8 20.8 - - + -
317C SER* 1.3 74.1 - - - +
319C VAL* 1.3 68.2 + - - +
320C VAL* 5.9 0.2 - - - -
347C GLY 3.3 10.3 - - - +
348C LEU* 3.9 8.5 - - + -
349C VAL* 4.9 0.4 - - - +
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Residues in contact with VAL 319 (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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112C PRO* 3.9 14.1 - - + +
113C LEU* 3.8 24.5 - - + -
308C SER 3.2 9.0 - - - +
309C TYR* 3.5 35.0 - - + -
317C SER* 5.5 4.3 - - - +
318C ALA* 1.3 82.4 - - - +
320C VAL* 1.3 66.9 + - - +
346C LEU* 3.4 5.2 - - - +
347C GLY* 2.8 53.9 + - - +
349C VAL* 5.3 11.4 - - + -
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Residues in contact with VAL 320 (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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112C PRO* 3.6 4.8 - - - +
113C LEU* 4.7 0.4 - - - -
307C GLY* 3.0 4.3 - - - -
308C SER* 2.9 40.3 + - - +
319C VAL* 1.3 79.9 - - - +
321C ASP* 1.3 66.2 + - - +
344C LEU* 3.8 20.9 - - + -
345C GLY 3.3 10.3 - - - +
346C LEU* 3.7 17.7 - - + -
403C LDA 4.5 24.2 - - + -
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Residues in contact with ASP 321 (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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111C PHE* 3.9 1.0 - - - +
112C PRO* 3.4 18.0 - - - +
113C LEU* 2.6 42.9 + - + +
114C TRP* 3.0 37.1 + - - +
305C SER* 2.8 23.4 + - - -
306C VAL 3.7 8.7 - - - +
320C VAL* 1.3 72.6 - - - +
322C TYR* 1.3 62.5 + - - +
343C VAL 3.5 1.2 - - - +
344C LEU* 4.4 2.5 - - - -
345C GLY 2.8 38.3 + - - -
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Residues in contact with TYR 322 (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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114C TRP* 4.0 1.6 - - - -
304C ILE 3.6 1.2 - - - +
305C SER* 3.5 4.1 - - - -
306C VAL* 2.8 58.9 + - + +
320C VAL* 4.4 0.4 - - - +
321C ASP* 1.3 71.8 + - - +
323C LYS* 1.3 70.9 + - - +
324C ILE* 3.6 11.8 + - + +
342C ASN* 3.5 25.6 + - + +
343C VAL 3.4 13.5 - - - -
344C LEU* 4.1 17.2 - - + +
403C LDA 3.8 56.8 + - + +
404C LDA 3.6 43.0 + - + +
421C LDA 4.0 9.8 - - + +
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Residues in contact with LYS 323 (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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33C GLU* 5.0 8.3 + - - -
114C TRP* 3.4 54.3 - - + +
117C ASP* 4.8 4.6 + - - -
303C TYR* 3.8 45.3 - - + -
304C ILE 3.6 4.0 - - - -
322C TYR* 1.3 72.1 - - - +
324C ILE* 1.3 62.9 + - - +
325C ASN* 4.4 9.6 - - - +
339C ASN* 5.0 4.5 - - - +
341C ASP 4.7 6.5 - - - +
342C ASN* 3.3 12.1 - - - +
343C VAL* 2.7 49.5 + - + +
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Residues in contact with ILE 324 (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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303C TYR* 3.3 3.8 - - - -
304C ILE* 2.8 49.1 + - + +
306C VAL* 4.1 28.0 - - + -
322C TYR* 3.9 23.8 - - + +
323C LYS* 1.3 72.1 - - - +
325C ASN* 1.3 62.9 + - - +
326C LEU* 3.5 8.8 + - + +
342C ASN* 3.6 13.9 - - - +
404C LDA 4.3 9.9 - - + -
425C LDA 3.6 59.7 - - + -
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Residues in contact with ASN 325 (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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302C LYS 3.3 9.8 - - - +
303C TYR* 4.0 9.2 - - + +
323C LYS* 3.6 8.1 + - + +
324C ILE* 1.3 70.9 - - - +
326C LEU* 1.3 70.3 + - - +
327C LEU* 3.3 23.4 + - - +
339C ASN* 3.0 30.3 + - - +
340C THR* 3.2 23.4 - - - +
341C ASP 3.1 21.5 + - - +
342C ASN* 2.7 21.9 + - - +
404C LDA 5.6 0.7 - - - -
425C LDA 3.8 18.2 - - - +
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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