Contacts of the strand formed by residues 300 - 311 (chain C) in PDB entry 5MG3
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 THR 300 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179C ASN* 4.4 19.1 - - + +
180C VAL 3.4 12.3 - - - +
181C GLN* 3.7 28.0 - - + +
295C VAL* 4.7 0.7 - - - -
298C GLY 5.4 0.7 + - - -
299C GLN* 1.3 79.6 + - - +
301C GLY* 1.4 61.0 + - - +
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Residues in contact with GLY 301 (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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179C ASN* 3.3 12.7 + - - -
180C VAL 2.8 34.1 + - - -
293C VAL* 5.9 1.6 - - - -
295C VAL* 4.2 14.9 - - - +
299C GLN 4.2 0.6 - - - -
300C THR* 1.4 73.7 - - - +
302C ALA* 1.4 62.4 + - - -
303C MET* 3.9 9.5 - - - +
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Residues in contact with ALA 302 (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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178C TYR 3.7 4.9 - - - +
179C ASN* 3.8 13.7 - - - +
293C VAL* 5.6 3.9 - - - +
301C GLY* 1.4 75.8 - - - +
303C MET* 1.4 68.2 + - - +
304C ASN* 4.4 11.2 + - - +
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Residues in contact with MET 303 (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 LEU* 3.6 26.5 - - - -
177C ASN* 3.8 1.2 - - - -
178C TYR* 3.1 46.2 + - + +
180C VAL* 4.3 9.6 - - + +
190C ILE* 4.0 24.9 - - + +
192C SER* 3.8 23.1 - - - +
268C ASN* 3.5 14.4 - - - +
293C VAL* 4.1 31.0 - - + -
295C VAL* 4.8 1.1 - - + -
301C GLY* 3.9 9.2 - - - +
302C ALA* 1.4 93.6 - - - +
304C ASN* 1.4 64.8 + - - +
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Residues in contact with ASN 304 (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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176C VAL 3.8 4.7 - - - +
177C ASN* 4.5 14.9 - - - +
178C TYR* 4.7 0.9 - - - -
266C PRO 3.7 0.3 - - - -
267C HIS* 2.8 43.9 + - + +
268C ASN* 2.8 19.3 + - - +
302C ALA* 4.4 9.5 + - - +
303C MET* 1.4 88.2 + - - +
305C SER* 1.4 62.1 + - - +
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Residues in contact with SER 305 (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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175C ASN* 3.6 5.9 - - - +
176C VAL* 2.9 31.6 + - - +
177C ASN* 4.7 0.5 - - - +
178C TYR* 4.4 6.7 - - - -
264C TRP* 3.3 29.4 - - - -
265C ILE 3.6 6.8 + - - -
266C PRO* 3.4 16.2 - - - +
267C HIS* 4.2 2.2 - - - +
288C TYR* 3.3 23.6 + - - -
304C ASN* 1.4 75.1 - - - +
306C THR* 1.3 65.2 + - - +
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Residues in contact with THR 306 (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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168C LYS* 6.0 0.2 - - - +
173C ALA* 3.7 30.5 - - + -
174C VAL 3.6 7.2 - - - +
175C ASN* 2.8 23.9 + - - +
263C ALA 3.7 0.2 - - - +
264C TRP* 3.6 6.5 - - - -
265C ILE* 3.1 46.9 + - + +
267C HIS* 3.2 27.2 + - - -
305C SER* 1.3 73.1 + - - +
307C LEU* 1.3 60.4 + - - +
320C VAL* 4.2 13.3 - - + +
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Residues in contact with LEU 307 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C LEU* 5.7 2.0 - - + -
79C VAL* 3.8 29.6 - - + -
110C ALA* 3.7 24.2 - - + -
165C PHE* 5.2 4.7 - - + -
173C ALA 3.7 0.2 - - - -
174C VAL* 2.7 49.2 + - + +
176C VAL* 3.9 6.7 - - + -
196C LEU* 4.1 4.0 - - + -
262C THR* 3.9 10.3 - - - +
263C ALA 3.5 15.0 - - - +
264C TRP* 3.7 28.4 - - + -
306C THR* 1.3 71.0 - - - +
308C TRP* 1.4 64.5 + - - +
309C VAL* 3.8 21.4 + - + +
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Residues in contact with TRP 308 (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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171C ASP* 4.2 7.2 - - - -
172C TYR* 3.8 18.6 - + + -
173C ALA* 3.7 40.4 - - + +
261C ALA* 3.3 25.1 - - + -
262C THR* 2.6 33.5 + - - -
263C ALA* 3.1 18.2 + - + +
265C ILE* 4.3 13.9 - - + +
306C THR 4.1 1.4 + - - -
307C LEU* 1.4 72.6 - - - +
309C VAL* 1.4 57.0 + - - +
310C GLY* 3.1 15.3 + - - -
311C PRO* 3.0 40.9 + - + -
313C ILE* 5.1 4.7 - - + -
316C LYS* 3.9 36.6 - - + -
317C MET* 3.7 26.6 - - + +
320C VAL* 5.9 1.3 - - + -
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Residues in contact with VAL 309 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C LEU* 3.4 41.4 - - + +
70C LEU* 4.3 15.0 - - + -
79C VAL* 5.9 0.9 - - + -
82C ALA* 4.7 7.2 - - + -
84C LEU* 3.4 7.4 - - - +
99C LEU* 3.6 20.0 - - + -
100C LEU* 4.1 18.4 - - + -
172C TYR* 3.1 16.7 + - - +
174C VAL* 4.8 5.2 - - + -
261C ALA 4.1 1.3 - - - -
262C THR* 3.6 11.7 - - - +
307C LEU* 3.9 22.4 - - + +
308C TRP* 1.4 78.3 - - - +
310C GLY* 1.4 56.3 + - - +
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Residues in contact with GLY 310 (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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84C LEU* 4.0 9.4 - - - -
99C LEU* 3.9 3.0 - - - +
172C TYR* 3.6 8.7 - - - -
260C PHE* 3.5 8.2 - - - +
261C ALA 3.0 32.5 + - - +
308C TRP* 3.1 9.4 + - - +
309C VAL* 1.4 76.2 - - - +
311C PRO* 1.3 70.3 - - - +
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Residues in contact with PRO 311 (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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87C TYR* 3.5 30.3 - - + +
172C TYR* 3.8 33.9 - - + -
259C TYR 3.3 12.3 - - - +
260C PHE* 4.1 2.2 - - + -
308C TRP* 3.0 26.4 + - + -
310C GLY* 1.3 82.8 - - - +
312C GLU* 1.3 51.0 + - - +
313C ILE* 2.7 38.4 + - + -
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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